[vishnu]

I did some progress by following the Administrator's Guide (.cshrc, .login, etc), but I am still missing a ton of things related to the more advanced applications, LIBPATHs, registration, etc..

You probably just need to merge the .chestrc files. For libraries, you can add a line in your ~/.profile LD_LIBRARY_PATH=$LD_LIBRARY_PATH:dirname - Where dirname is the directory in which the libraries reside.