If you mean changing the base colour using the in-game editing options then thats easy.
You have 4 different colour options with each set of boots you make. They are located under colour pattern and named 1,2,3 and 4.
If you select any of these it takes you to a screen with a picture of a boot in a big rectangle and 8 other smaller boxes. If you select the boot rectangle and press X this allows you to change the base colour of that boot.
Hope this helps you.