It boils down to this... It's as hard as you want to make it.

The easiest thing to do is to cover your plane 1 color, but it's not recommended.

A two color scheme allows you to have the needed contrasting colors that enable you to see the plane better against light/dark backgrounds.

The more colors you add, and the more complicated the design, the more difficult it becomes.

To do things like line up one side with the other, you simply measure from a specific point ("ok, the red stripe ends 3 1/2" from the end of the aileron, so it has to be the same on the other side". Etc.)

Sometimes it's easier to put a detail, on top of the base covering, and sometimes it makes more sense NOT to have covering under a trim piece. Every color scheme is different.

You can even do the same scheme several different ways. On my first Ultra Sport, I had a blue band with white stars on top of a white base. I cut the stars out of the blue to let the white base show through. On the second one I built, I added white stars on top of the blue. So in many cases, the choice is yours.