Clean the PE parts with preferably denaturated alcohol(not Isopropanol A.K.A. rubbing alcohol). If you don't have denaturated alcohol and can't get any, then use soapy water, but don't let the water sit.
What type of paint are you using? It sounds to me you are using way to much paint and trying to do it in one coat. I have never had paint cover the detail on photo etch parts.