Ok this is the way I have been doing mine sorry for the blurred photos but I think you get the idea
Ok I start with the head painted and the tail tied in
Now tie the back end color in note just like you would the main color but stop short when raping channel like two turns and then run the thread down and lock it in then trim the first color tab run the thread back to the head
Tie in the second color just before the first color run the thread to tie it in then back up to the head
Run the second color to the head and whip finish it
When you do the back color think of it as that is where the head is then when you put the second color just tie it like you would any jig.
I keep looking at this and well I hope it makes sense ask ? if not.