When using TC you need to keep the folder structure intact, the AZP pluging can't handle it otherwise. So if you need to put a file in a folder inside the AZP archive you need to copy the folder too. If the file inside the BMP.azp is in \BMP\HUD\file.tga you need to copy the BMP with the subfolders and files inside it.
I'm not familiar with the MoP file structure, but it might work similar to how 7.62 does. In that case you can leave your edited files outside the AZP archives and they will take presidence over the files inside them. Just make sure the have the same folder structure in the game folder as they had in the archive.
Good luck
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