When you say that you "want to paint transparent pieces," can you provide us with more detail about what specifically you are trying to paint?

That is, are you trying to paint a canopy frame, putting color in very smaller areas but leaving much of the piece clear?

Are you trying to tint a windshield, so, you want color over larger areas, while keeping a level of translucency?

Something else entirely?

Depending on the desired result, perhaps markers aren't a good tool to use.