I have used the windex method with mixed results. It works ok if the second color is not a large section. (i.e. trim lines & shapes)

I have a method that works extremly well for me expecially over open areas. Get yourself a large section of glass (my piece is a windshield out of an old school bus), tape the edges for safety. Lay out the monokote pattern for the whole wing panel allowing a 5mm joint for seaming. Lay the first color down and smooth it to the glass. Lay the second color down on top of the first allowing a 5mm seam and smooth out.

Now comes the tricky part. Take a monokote trim iron (the small one) and start seaming the seam. Start in the middle and work out to the ends. Don't drag the iron along the seam as it will cause wrinkling. I start by just placing the iron on the inside portion of seam and rolling the iron to work out air to the edge. Then pick up the iron and do the next inch. after all of the seam is done, go back and reiron the entire length of the seam. Look at the seam at an angle to the light and you can see if it is completly bonded.

Then remove the complete panel from the glass (lifting perpindicular to the seam) and install to wing panel. If you seamed correctly, you can stretch the monokote with no fear of the seams seperating.

I have done multiple colors (4) in very complex patterns with exellent results. After shrinking with heat gun you get a bubbleless mirror finish including seams. I have covered 8 different airplanes using this method.