Applying two patches at the same time on the same ROM - possible?

Hi there, I figure this might be a pretty noobish question, but still. I'm trying to get my Inazuma Eleven 2 Firestorm ROM AP-patched (with that DS-Scene tool) and Remaster-patched (with xdelta). Now I've tried this sequentially, and it didn't seem to work. I've tried first applying the AP patch and then the Remaster patch, and vice-versa, but on both occasions the first patching already altered the ROM in a way that made it illegible for the second.

Is there anyway to work around this?