For water based fillers, you can tint it with RIT dye. Mix the dye in a separate cup and add it to the filler a little at a time and mix it in until you get the color you want. You can mix it in an ounce of water and add dye by the teaspoonful until you get a concentrate darker than the color you need.

Get RIT dye at the grocery store or crafts store. You can also get water soluable dyes from Rockler, Constantines, Woodcraft, etc. Jeff Jewitt also carries them at his site ( www.homesteadfinishing.com )

NEVER use oil based stain or fillers under epoxy or fiberglass - the epoxy/'glass either won't stick to it or it will adhere only until stressed and then it'll let go.