Make your sprites greyscale, and use Color tint effect.
Take a look in the tools section of this forum, I added a template for node webkit + the sources.
in the sources you will see how I did a color pallet, and mixed the colors to the sprites.
If you want to go a step further, make your sprites greyscake except for key colors.
Use a tint effect to color the greyscale, and use a color replace to change the key colors.
All of the effects use the same values so it is easy.
Rather than 255 shades for R,G, and B, you will have 100 as the ceiling and 0 as the floor.
It is a real pain in the $#@ to adjust because you need 3 event actions for each color change.
effect parameter 0 is red, 1 is green and 3 is blue.
hope this is useful
EDIT there is a Set color too, that is really nice for making pallet color swatches, and anything else you need solid changeable colors for.