Hi Steve,
I can't really help you with the rpm issue except for the fact that I setup an ibay solely for the purpose of storing downloaded files. I mapped a drive on my windows client to the ibay, and then I just select the ibay files directory to store the download. I then move these files to the directory I want to use by using the cp command from the command line (I do this by using putty and ssh).
As for PHPNuke, I had no problems installing from a tarball. There are a few steps in the process (create a db, execute a few sql files, set some file permissions), but if you follow the directions its pretty easy. Do remeber that if you want to enable php in the primary bay you need to enable php by applying one of the rpm in the e-smith rpm list (can't remeber the name of it but its easy to find).
Hope this helps,
John Goodwin