To have different textures on each side, all you need is to do as I mentioned before and give the outside texture A and the inside texture B. When done texturing, move the polygons back and merge the vertices.

As for many different textures on the inside, my tutorial covers this (for the grass area). To have multiple textures for one model, just lay the textures out on the skin as needed then just move the skin vertices of the part in question to the texture needed. There isn't much to it. See how I have the textures laid out on the skin?

As to other modelling software, I have no experience with them at all so I don't know anything about Wings3D, 3DS Max, Blender, and whatever other modelling software there is. MED was the first modelling software I've ever used. Someone else will have to help you with that.

Also, I wouldn't recommend using any texture size above 1024x1024, mainly for compatibility reasons. 6.4's MED allows for easier texture tiling and you can assign multiple texture files to a single model. They should also always be a power of 2 (use 2048x2048 instead of 2056x2056).