The simplest way to paint a polymer clay piece is using acrylic paints over a primed base. Priming
There are two basic types of primer to use on polymer clay, spray primer and gesso.
Acrylic spray primer is very easy to use, simply aim the can at your sculpture and spray taking care to make an even coat. Make sure you use spray primer in a well ventilated area, spray paint fumes are hazardous to breath. Krylon acrylic primer works quite well, it comes in 4 colors white, black, gray, and rust brown. Pick the color closest to what you want your finished piece to be. For example light skin tones white is best, rust brown can work for dark skin tones, black works well for dark colored vehicles or monsters, and gray for anything in between.
Acrylic gesso is a thick textured paint used to prime surfaces for painting. It comes in two basic colors, white and black, but the white version can be tinted using acrylic paints. Gesso is very thick and gives a beautiful surface to paint on, however it will fill in fine details so it wouldn't be used on textured areas. You can even use gesso to paint on details like veins.
Painting
I recommend using artist acrylics rather than craft acrylic which are lower in quality than artist acrylics. Student Artist Acrylics are in the middle when it comes to quality but at a reasonable price and a good place to start if on a budget. Tube acrylics are very thick and need to be thinned with acrylic medium or water. I prefer Golden Fluid Acrylics which have a smooth consistency a little thicker than heavy cream (there are also other brands with the same consistency try them out until you find one you like).
Acrylic paint dries very fast so you have three options if you aren't a speed painter.
1: Squeeze only a small amount of paint onto your palette at a time.
2: Use a stay wet palette (any art store and most craft stores carry them or you can make one)
3: Use acrylic retarding medium which keeps the paint from drying as quickly (buy where ever you get your acrylic paints)
I find it best to gradually build up color in layers using a barely damp brush or makeup sponge. If you've never painted before you should check out some Basic Painting Skills or the links below.
When finish I seal my sculptures with Testor's dull coat for a matter finish, Krylon crystal clear for gloss, and krylon workable fixative for satin. Small glossy areas like eyes I use Delta gloss varnish.