You can go as deep as you want. Polys live in deeper water then our tanks so don't worry about that. But make sure there is enough room for them to breach and gulp air. It's seems logical that if swimming in open water they'd feel more vulnerable so less height is probably "better" but they are still going to get air, just make sure they can.
As for decor up higher some of mine seem to love sitting up higher. I have one spot on my background that sits about an inch below the surface. My albino loves to sit there, his back is just below the surface.