Oh, hello there.
I was directed to this thread by the lovely Bond697, and to be blunt, I'm eternally grateful that this exists
In case this helps anyone who may have trouble in the future;
I had some issues with it at first, but I found a fix in the DSTT savegame_manager edit a couple pages or so back.
I have the original R4, I'm very sure of it - so I don't know why it refused to recognize savegame_manager.ini. After some playing around, I used http://projectpokemon.org/forums/showthread.php?12405-A-tool-to-backup-HG-SS-saves&p=115386&viewfull=1#post115386 and it worked perfectly. Again, I have no clue why, but hey, why complain? It took about 40 minutes to back up both games, 20 mins each. I haven't tried restoring, but I'm sure it works fine.
Using a DSLite, HG/W U game, with an original R4DS, and 1.27 R4 Wood kernel.
Hopefully this provides some aid to another person in this situation.
Again, a thousand thanks. You have no idea how much you've helped me. (: