-drag the rom onto the 3.1 exe.
-burn either the nds_save or gba_save (more likely only the nds save will work) to a Neo or XG cart.
-put a DS game with 2mbit save size into the Magic Key/PassMe/DS slot if using flashme (a game like splinter cell or Madden so it has the right save space to store to)
if its going to work, that is how to do it. I had it going with 3.1, nds save and madden 2005 in the DS slot (using flashme).