It has been said many times, use the 996 USAD program, map the database directory to the 396 database folder and then use that to update the 996 information if you want to specify GPS, etc. Using the 996 program you can make changes to the 396 files, if you then go and use the 396 USAD program it will wipe all settings from 996 program if you make modifications using that, you can just upload using the 396 program to the 396 and that should not effect the 996 changes to the system files.
If you want to have different 996 and 396 files then open the original 396 file in 996 USAD and use the save as, rename the file and you are done.
Hope that helps, there has been many a thread on this, so you can do a search and get more.
Your welcome, my other suggestion would be to keep it as simple as possible at first.
There are a lot of options and such, it could get overwhelming, go slow and read the manual and do searchs here and on the yahoo 996T group. Most of everything has been said at least once at this point, along with discussion on features.
Good luck and enjoy.