I've found that spending the extra effort to submerge skulls goes a long way to making them look better (and if you're cheeky, this can let you get two for the price of one sometimes ). In your case some non-tiled or broken bits to "embed" a skull in would work best. For the tiles the skulls would sit on top, so that's actually easier for it.
I agree that you don't want too many skulls, but that just means you need other bits. From water effect (which is really good as it can work with anything), to various other bits or helmets you can keep the variety up. Maybe chopping up some sprues to create some rubble/masonry would be best as the more standard piece?
If you have spare slot bases (I think everyone does? ) trying out ideas on them is a good idea, it's how I trial my basing schemes without risking any models