Basically, you can find this information in a few other places, but it took me a little while to find, so I thought I jot it down, so I remember and in case someone else thought it was useful.
First of all, I want to thank Kirk Haselden for his fine book on SSIS. It has truly been a lifesaver in developing SSIS standards for a customer. In his book, Kirk talks about the "magic folder" for SSIS. This is the folder where the SSIS Server looks for packages. Essentially anything with a .dtsx extension will show up in SSMS when managing an SSIS instance. By default, this is a folder buried deep in the bowels of Programs Files, namely C:\program Files\microsoft sQL Server\90\DTS\Packages. This is a relative path to the install (..\Packages), so it can also be moved if you move the install location for SSIS.
Just as Kirk describes in his book, you can change the location of the magic folder by editing the config file, MsDTSSrvr.ini.xml, changing the StorePath value (p.383). You can also add more StorePaths to have multiple file locations for SSIS to look. But you can get this just by reading the book...
Now for the good stuff. We wanted to have a known location for our SSIS packages, not the relative path that comes in the default config. We wanted to hang the store off the root of the E: drive in the SSISPackages folder. It wasn't documented anywhere, but there was a hint of it in Kirk's post about clustering the SSIS service. The path doesn't need to be relative, it can be hard coded to a drive letter if you like. We changed the StorePath value to E:\SSISPackages, restarted the SSIS service, and voila, we could see packages in the folder via SSMS.
Again, you can find this information in a few places but it wasn't explicit. Hope this helps someone other than me.
Jon