Need help merging textures

My WIP levelset is using a handful of different texture packs--Too Much Brown, Doom 1 textures for Doom 2, and the Recoloured Doom Texture Pack from R667.

My question is, how do I combine these three properly to distribute when I release my WAD? (I'd also like to combine them for my own purposes so I can just load one WAD as a resource instead of all three.) I tried just copypasting them all together but I got several duplicates of the default Doom 2 textures; is this okay or is it a problem?

Any help would be appreciated.

Use WADMerge: http://www.teamhellspawn.com/exl/?page=wadmerge
There is also a new supposedly advanced version but it doesn't even have a window interface, so I'm still using the old one.