Probably the biggest tip I can give you is do EVERYTHING in a new layer. Whether it's adding a new color, logo, or whatever. Always do it in a new layer. Here's a good example:

This template has 16 different layers on it. All the base colors, logos, numbers and lines have their own layer. What this does is it lets you easily adjust and reposition any part of your repaint in just a few seconds. It also saves you a huge amount of headache if you screw up on something since having to delete and redo only one layer isn't usually a big deal.
As for getting everything lined up, well that's really just a process of trial and error. And it's where the RW_Tools asset viewer really comes in handy. It will let you quickly preview what your repaint will look like in-game so you can make adjustments to it. It's much quicker than loading up a route in RW just to preview your repaint.