If I'm only going to need one colour of fondant, I add it at the making stage - otherwise you just have to knead, knead, knead! Pop it in the microwave for a few seconds first, it makes it easier!
I use the gel paste and a toothpick and then knead the fondant until the color is all blended through. If you are worried about getting the color on your hands then you can wear gloves.
I used my hands and it was hard but I finally worked the color in . Then I saw on CC that you add it when melting the marshmallows . The next color I needed I let the KA with the dough hook do the work . From now on I will add it in the melted marshmalllows .
HTH
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