RIT dye powder is what you needed so you're OK. Mix it in a separate cup with some water and add that mix to the putty a bit at a time. Use HOT water (boiling is ok but not if the cup is styrofoam or thin plastic - those'll melt at that temp) and don't worry if all the clear beads don't all disolve. They're not color adders so it won't matter if they're mixed in or not.

Some people have stated that analine dyes are better than RIT because the analine dyes won't fade in sunlight. I'd not worry about that since the varnish on the boat needs to have UV additives to protect the epoxy it will also protect the dye. Also, if you read the box, RIT says that the dye is made to resist sun fading.