OK I'm going to lay out a lot of stuff here in chronological order, this is not a complete replacement for the guide and this does not tell you every step required. I am describing how the SGI partition table works in heavy detail because it's actually very important. After the partition table I am loosely describing the installation start process. Depending on if you have a SCSI CD or DVD drive and you're burning CDs or if you're doing a network install and you need to CD file tarballs - those are two separate installation methods. I only use the CD method myself so I can only provide assistance with that. The guide goes specifically over CDROMs, the network install is an expansive version of the CDROM install. You need to understand the CDROM install to understand the network install anyway
DISK LABEL = PARTITION TABLE, but implemented in a highly special way that only SGI ever did.
MIPS SGI platforms use a special designed partition table/boot image storage/etc implementation that is called a disk label, they are similar to a partition table as used in a personal computer but they are implemented very very differently. Remember this was pioneered in the 80s. The original disk label is able to actually address 1TB (before Irix 6.5.15, then 2TB) back when PCs could barely address a tens of Gigabytes. The label is not just on the front of the drive it is actually strewn throughout the volume of the Disk. So it's actually hard to get rid of one!
On a PC you can just overwrite the 1st MB or two and technically blank out the partition table to make a utility the disc is empty, that does not work on an SGI disc label! You actually have to overwrite quite a bit of the disk with 0s to get the label to disappear, if you want to drive to appear blank. But you can however create a label and overwrite the old (existing) label! However if the label ends up being identical to the old label you can actually wind up with data surfacing from the old install into the new one. This can be a big problem. But if you go from an option disk to a root disk this can't happen. There there are a few different ways to blank a drive if you're running into merging issues with the old data and the new data mashing together because the partition tables were identical between new and old. You can either overwrite the entire drive with zeros using another computer or you can use FX and exercise to drive using the exercise menu to write sequential zeros to the drive for you. Since you're using an SD card adapter this all basically means please create a brand new HDD image image on the SD card, do not attempt to reuse your old image file you could easily run into this type of problem from an old install and a new install actually merging together.
The disk label by standard has several partitions, they are numbered and also the numbers tend to be assigned various duties. You do not mess with the numbers, they are not random, and they are not for your choosing. They are not meant for the user to decide what each number does what function. This is similar to the way PCs are now provision with GPT for EFI operating systems, but with more partitions.
Messing with these numbers almost never works out well, even if you know what you're doing. By default FX does what you want to do and either creates almost all the space for the root file system (/) or almost all the space for a file system that will later be mounted at a point of your choosing that is NOT a bootable (ROOT) filesystem. But mounted anywhere else such as: /opt, /usr/, etc. You do not normally fool with the other partitions or how much space is allocated to them. You do not mess with their order even if they don't appear in chronological order.
There is only one ROOT partitioned disk per system, there is 0 to however many additional disks the platform supports of OPTION disks which is a file system that can be mounted to any other mount point but can never be the booting drive and can never be the root file system. You always start with a single disk system as a root formatted drive. You then format option disks to add additional drives to mount points on the file system. Irix does have a logical extend volume manager but it requires a license, so no one uses it. I don't believe you can boot off it anyway.
Unlike other partition table standards, SGI partitions may overlap each other on an SGI disk label. That means that some partitions are in fact a subset of one another. They are designed to have different views of the various places on the hard disk. So writing into one may actually affect another partition's contents. The numbers have important meanings:
While that's not etched in stone, their meanings are roughly:
Partition 0 is often ROOT / (XFS or EFS in older Irix), largest partition on a ROOT DISK.
Partition 1 is often SWAP space (RAW FS)
Partition 6 is often /usr, or on an OPTION DISK it is the largest partition to attach elsewhere on the main Filesystem. So this the largest partition on an OPTION DISK!
Partition 7 often represents the ENTIRE READABLE DISK AREA, EXCEPT the Volume Header and the XFS LOG.
Partition 8 is the VOLUME HEADER (VOLHDR), this is a critical area where the disk label itself and the boot image information resides, including the kernel image that's actually booted from firmware and (optionally) independent bootable diagnostics on some systems.
Partition 9 is reserved (if exists)
Partition 10 is the ENTIRE VOLUME, all the PHYSICAL WRITABLE DISK, INCLUDING VOLHDR AND XFSLOG, more than access than Partition 7, everything!!!
Partition 15 is for XFS file system transaction LOG (if exists, used on XLV volumes, MAY NOT BE PRESENT ON SINGLE DISK SYSTEMS, used in XLV)
As you found FX is a very rigid program and has expert features only for rare cases. Please follow the install guide but generally the order is this.
On a single disk system you will boot the overlay disk Install image/CDROM first along with all the other required discs of which there may be many of them, much more if you're doing developer/compiler work.
You boot FX and specify controller 0 disk 1. You're single driving in your Indy should be at SCSI ID one, if it's not jumper the drive correctly so that's is the case. At the FX prompts you basically say that you would like to re-partition a drive, you want a [RO]OT drive, not an option. It will actually suggest defaults to you even though it shows a blinking cursor there's a default suggested you take that default, the defaults are always the maximum size the drive allows for the single volume you're interested in. In root disK it makes the root partition 0 the largest and on the option disk it makes partition 6 the largest using the volume you've presented. You do not nor have you ever needed to actually type in the space required for your partitions, it's in cluster sizes and it's highly confusing.
TAKE THE DEFAULTS! (This all in the guide):
http://www.sgidepot.co.uk/6.5inst.html
[R]epartition > [RO]OT > Confirm XFS > type .. to go back up a level > [L]abel > [Sy]nc > type /exit to quit.
You're done partitioning, it was that fast...20 secs.
The rest is the tricks of loading the OS without getting errors due to conflicts or when you boot. Remember the OS was not meant to be installed by the end user this is not meant to be a user-friendly process was supposed to be done by an on-site SGI tech or a trained administrator. Treat this machine more like a CNC milling machine or other appliance not like a personal computer. Several aspects of this process will appear very unfriendly to the average user, SGI didn't care about that because you were supposed to have a support contract and you weren't supposed to be fiddling with the operating system. That's why this process is not as easy as say installing Windows or macOS.
There are several places you can get the disc images from archived.org and WinWord are two good ones. The CDROM images by default are not meant to be unzipped and readable they use a special format and use EFS. You cannot normally mount them or see inside their images without special tools. Using a CDROM install is physically the easiest method if you have a SCSI CD or DVD drive or you have one of the more advanced Zulu SD adapters that can emulate CD-ROMs. If you want to do a network install you'll need to find the files that have already been pulled from the CDs into tarballs. Someone else may be able to help you with that it's not my thing.
The CD images or the files need to be fed into the install process in the order stated in the guide, the order is important, it is not arbitrary. The guide will also suggest how to prevent packaging install conflicts toward the end of the installation process, it's an important step as well.
Start the process first and see how far you get and then return back. If you don't plan on doing any development work or compiling software you don't need to install the development foundation files. But if you have the space and you have the disc it doesn't hurt you to do so. Please get the CROM images indicated by the install guide and start the install, use FX as recommended, and continue the install as recommended by the guide.
NEED -> 
Going forward, would reading something like the manuals on Techpubs help me to learn more about IRIX? I do need to get my head out of the DOS/Windows gutter and learn more about UNIX.