Quick Instructions:

Get the template for the object you are making it for

Put it in a Graphics editor like Gimp or Photoshop as layer 1

Put the actual texture template as layer 2 (under)

Put a layer 3 all white on the bottom (turn off)

Turn the opacity of Layer 1 (on top) down so you get a grid on the of the template on the texture

Make a new Layer 4 on top that is transparent.

Paint black things you dont want to see

When done, turn off layers 2 & 3, and save as a jpg (Black on white)

On the materials tab, plug it into the transparency node, and increase the value to 1.0

BAM!