The "base mesh" when references by MH is the 3d model defining the human. It consists of some 18000 coordinates which in their turn define surfaces.
In blender you can basically paint anywhere on the 3d model. The result end up on the skin texture looking like this:
http://www.makehuman.org/sites/mhnew.jw ... exture.pngNote though that if you don't like the way the skin has been "unwrapped" here (ie where the seams were when it got flattened to a 2d imag) blender allows you to draw seams and make another unwrap.