the world, boot5zones, etc.. should be in eqemu folder, there are like 2 or 3 other folders for editor and stuff, they can just stay in the folders. If it didn't not overwrite anything, it probably made another folder. Just cut/paste it out and back into the eqemu folder to overwrite the older files.
*edit* I am not sure what folders there should be, I don't have eqemu on this machine right now.
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