If your files have not got partial changes in them, for example, one patch has units.dat modified to make a powerful Zergling, and another patch has units.dat modified to make a powerful Goliath, then it's quite easy. Open the EXEs in WinMPQ (it's more than likely the EXE is just an MPQ, try it) and extract out all of their files. Then import all of the files that you extracted from the two MPQs into one MPQ.
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Okay, then why don't I just put the .mgd file in my mod folder in the first place?
Anyways, the mod and the patch_rt.mpq files are different.
As I understand it, when you use the *.exe file made by MemGraft, it tells it to load the modified patch_rt.mpq with your modified buttons in it.
Patch_rt.mpq and NovaCraft.mpq are different *.mpq's with different files in them...
That's a bit different. In the first case, which I answered before, the key word is -merge-. That's saying "I want -all- the changes in A and all the changes in B in one mod." In the case where you're creating a MemGraft mod, it's more of a "I want -all- the changes in my mod, and everything I didn't change I want to leave the same." So with the first one, you want all the changes of both mods to appear in the final mod, neither MPQ file takes precedence.
However, in the second one, you only want the changes from one mod, and to use StarCraft's original settings for everything you didn't change. In that case, your mod is taking precedence. You're manually doing what StarCraft does when it searches two MPQ files, one with a higher precedence.
EXE2MPQ is designed to work on EXEs that were created based on CWADs. We haven't used CWADs for years now, it's unlikely you'll ever need to use EXE2MPQ.