no, supercard and neoflash are not the same items.
It sounds like you have an older firmware version that is compatible with PassME1 (assuming it turns darks green - that's FW3 which should work fine)
Now, for Neoflash 3-1, procedure should be the same:
1) For gba mode, double-click the gba mode icon on your desktop. Open Neo Power Kit, and burn the gba roms you want to play (including that neoboot.bin file, which is a gba loader) onto your flashcart.
2) For nds roms, double-click the nds mode icon on your desktop. Then, patch a single clean dump using gst-patcher 3.1. Using Neo Power Kit, burn the gst-patched rom. Use the gba_save version (if you want to save to the flashcart) or the nds_save version (if you want to save to the ds game cartridge -- though you need to match the size of the save file to that used by the game cartridge)
3) If nds rom doesn't work, it's probably because the patcher isn't compatible with that game.
If you have done all this, post more details about the problem...
BruceG