... Let's take a 16K ROM. I guess I have to supply it as one file and not two files. And that answers my question about how the logic works in the FlashROM99, - one file equals one game equals one entry in the FlashROM99 menu !?
Well—it doesn't have to be a game; but, yes, one file (32KiB or less of non-inverted banks) equals one program equals one entry in the FlashROM99 menu.
... And entries/carts that have their own TI menu is no problem. After selecting the entry via the FlashROM99 menu, the system simply boots with that cart in place !?