Well first off, you usually want to create and export your UV map from your model into an image. Then, you can paint it in Photoshop or Painter, and then you can apply it as a texture map onto your model.

Here's a great tutorial for 3ds Max users:
http://www.3dtotal.com/ffa/tutorials/max/UVW_mapping_an_object/UVW_mapping_an_object1.asp