AHow do I keep the color from running/bleeding as I paint on MMF?

Could you describe what you are painting?  Is this during the painting process?  Or does this happen after the paint has been left to dry?

AThis happens while I'm painting on MMF. The fondant almost acts like I'm painting on a paper towel.....

What are you using as paints?

When I paint on MMF I mix the food gel or paste with a bit of 100 proof Vodka. It evaporates very quickly and leaves the color on the fondant.

ADo you let the MMF completely dry/harden before you paint?

Craftsy is offering a free class on painting a cake.  You may want to take advantage of it.

http://www.craftsy.com/classes/cake-decorating

AGoreti, thank you for the heads up and the link!

It sounds like it could be your paint.  What are you using?  Like lolarx8 suggested, food coloring gels + alcohol work well.  Sometimes I paint with airbrush colors (w/o the airbrush, you know?) straight from the container.  You want a color agent plus something that evaporates quickly like clear alcohol (e.g. vodka, Everclear).