rather you paint over or under them it probly dosn't matter.. what program are you painting in ? you might should try to paint over if you are unsure how to make sure the right layer gets saved as the BMP. well anyway.. when you save the texture out of your paint program make sure the wire is not visable anymore and save with out layers or alfa in a BMP..

in your UV texture editer, over the UV's ,right mouse button press and hold, drag over to UV's. after that is selected .. when you try to select whare the vertixis should be , the UV points will be there.. in green.. selecting the points just like you would vertixs.. you just use your move,scale, and rotait tools like normal with it..
Hope that helps.