Are you booting the Supercard in DS mode or GBA mode? If in GBA mode, you'll see the *.sav file in the Saves tab but you won't see the *.dsq converted ROM file. Do converted GBA games work?
To boot a slot-2 cart in DS mode, you need either a slot-1 homebrew device that can do it, or you need a slot-1 "NoPass" device like the Superkey or PassCard 3. Once you do that at least once, you can install FlashMe on the DS which will let you boot it in DS mode just by holding Select rather than needing the slot-1 device.