All depends on what you need and are most comfortable with - and what your shader dictates. I generally prefer to work from the concept (all the textures in place and working) to the individual parts. You can do this by using channels in Photoshop to act as masks. This way you can see more or less what the composite skin will look like in 3DGS. After I get what I want, I make sure the channels are in the proper RGBA positions and then go ahead and save it out as my blend map for use in the shader.

http://steempipe.technicalfoundry.com/terrain/terrain.html (example of shaders using more than two textures on the terrain)

In theory you could use as many seperate textures as you want. Each one needs to have its own channel for blending though (and you could add more and more blend maps till you drop to 1 FPS and 200+ MB of memory being consumed). In practice though, you should probably stick at or around the 3 or 4 mark. Anymore and you really start to take heavy hits on the FPS as the textures are processed.