I do my pages the same way you describe, Crystal.
But I don't think I've ever seen the black box problem in my PSE-5.
Can you take a screen shot and post it? At the top, are the little boxes "Auto Select Layer", "Show Bounding Box", and "Show Highlight on Rollover" checked? (they are on mine) At the right, are your Layers visible? When you say you can't layer anything, does that mean you just can't click on them? I'm sure we can figure this thing out!