I'm with old paint on the clear transfer tape. I tried to use registration marks once and never will again unless it's an absolute must. For one, you can use more vinyl and waste more time having to add the needed registration marks. Besides that, if you have a good eye and a little patience you can figure out how to apply the second layer of graphics wet and line them up that way. I will usually wet the vinyl and the substrate and apply from the center out toward the ends. As I lower the ends of the graphic toward the substrate I can shift it one way or the other til the ends fall into place. If not, I pull it away and try again. Most times I can get it laid on perfect the first time around. Some people may agree that wet application isn't the best method. In my opinion wet application traps more air bubbles than dry application, but it's one of the fastest, easiest ways to line up multi-color graphics.
The only thing I don't care for with the clear tape is, at least from my experience, it doesn't release nearly as nice as paper transfer tape, so I generally use the paper tape more than the clear, but the clear has it's purpose, especially when applying multi-color graphics in a low contrast situation.