I pre-wash all but the pre-cuts. There have been a few horror stories from gals on here that washed the pre cuts. Tangled nightmares were what they called the resulting mess. I think you might have better luck hand soaking any questionable colors of pre-cuts to see if they did bleed. That would control the agitation and still let you see if they wanted to run before you incorporated them into your quilt.
I'm working with my first pre-cut quilt now, so we'll see if it makes a difference if you mix washed and unwashed fabrics together. I had pre-washed fabrics in my stash that I wanted to use with a honey bun, so I am giving it a try.
I have also heard good things about the color catchers. I use a cup of vinegar in the rinse on fabrics I think might have a problem holding their color. It's supposed to help set the color and work as a fabric softener. The fabric feels fine and does not smell like a pickle when it's finished!