Since you plan on painting, why don't you use Koverall instead ?
If you want to stay with the Coverite, use latex to paint it. Latex is compatible with everything. Here is a link to an excellent article by Roy Vallencourt on painting with latex.
http://www.modelairplanenews.com/how_to/latex1.asp
If you decide to paint with latex, be sure you add 1 1/2 caps of FloTrol per quart of undiluted paint and spray at 25 - 30 psi.