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Blacksmith 3D Paint can do what you want, and the basic version is free. Here I opened up V3, and clicked my butterfly onto her back. Look on the right side at the resulting color map. You can see that the program took the image apart for me and rotated and scaled the butterfly in two pieces to make it work out seamlessly. You can do this across material zones, too, like head/neck/torso.

The program is a little tricky to learn, but very powerful. The free version will not do above 1K by 1K on a color map, though. For really high-res work, and also to enable all the tools, you should buy it.

I was wondering how you import this butterfly to the program... I keep trying to do it but it always appear as a nem map...