As someone else said the Ewin GBA loader works fine with the DSTT GBA pak. Grab it
here.
No need to pre-patch GBA games at all, the GBA loader will do all that for you automatically. Works pretty well, just stick the loader on your card along with a few GBA games.
*edit* more details.
When first booting a GBA game the Ewin loader will load the game to the card then it will automatically patch the game then apply any save patches the game needs (it will auto-detect if it needs a patch or not). The second time you run the game it will just load the game to the card without going through all the patches as it's already done. It doesn't look like games can be kept on the GBA pak, they have to be loaded each time. Thankfully it's pretty quick loading. A 32mbit game loads in just a few seconds and a 128mbit game takes about 10.
Save files are written to the microSD card, no backing them up required when changing games and no fussing about. I'm really liking it so far.