I have a certain frog that just plain catches but after 2 seasons the color is needing touch up....can you paint soft bodied frogs and if so what should I use?

i wouldnt do a thing to it.  If you try to paint it and screw it up, you will be ticked.  The paint could hinder the action of the frog.  If you feel you need to do something, I would look at using Sharpies to add color.  I however would not paint it though. Seems like baits that catch a lot of fish, will catch them with screwy paint jobs as well.

Is the bottom messed up or just the top?

I vote dont bother

Unless it doesn't work, or stops catching fish, I wouldn't do a thing. I'd go pick up a new one if either of those is the case.

It is cosmetic. I want some color breakup to accentuate movement.

i would use either soft plastic dyes with Qtips or a sharpie. They have so many sharpies you can use any color and its easy to control