Currently, you need to go into the Atari800 menu (either by pressing F1, or by selecting the ATARI Joystick in the Controls quick menu, and then pressing R), go into Emulator Setup, and tell the emulator to look for roms in your system directory.
There was a patch for this, but it looks like we need to go further with it (and do a rom scan upon initial run).
Once this is done, you should probably go through each of your 5200 games, run each one, and set the appropriate cartridge type, and then press F1, go into the cartridge menu, and save the cartridge. This saves a header on the cartridge so you don’t have to re-set this.
(so many 5200 cartridges, and atari 800 cartridges are raw dumps, without any mapper information. To solve this
without forcing ROM librarians to start carrying cartridge images with a header will require an internal hash database with the appropriate mapper parameters, I’m considering this…)
-Thom