Yes, just knead it into the MMF like you do with regular fondant.
It's easier to color during the melting stage. You just have to realize it'll be a little lighter once the sugar is mixed in. But, it's also fine to color an already-made batch. Just takes some elbow grease. And I've not found a way to do it without making a mess, as the color squishes out the sizes the first few turns of the dough - whether I use paste or powder...big mess.
If you wnat to avoid teh color squirts you can put it in a ziplock and kneasd just unitl the color is oncorporated enought not to squirt out all over your hands.
I just made fondant for the first time last weekend and forgot to color the marshmallows after I melted them, so I just put the finished fondant back in my Kitchen Aid mixer with the dough hook and put a couple of dabs of color in with a toothpick and the mixer mixed it for me. I tried hand kneading it first, but it seemed like it would never be done, so that's when I tried the mixer.
wear gloves and get ready to work that fondant!!
Been there done that.
Don't walk around your house as you knead the stuff either! I found red drops of color on my carpet!!!
It will take a while but it can be done. Good luck!
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