Lutra, I would arrange the rock so that it isn't piled-up against the glass. Not because I'd be worried about the glass, but because you want to make sure you have good circulation in/around your rockwork to prevent detritus build-up.
Cjsrch, please don't make the mistake of thinking you're the only person here who has experience with bioballs or wet/dry setups. Plenty of people here have been around the hobby a lot longer than you and are speaking from experience - not simply "spitting up what they saw others read".
Bioballs offer powerful nitrification with no denitrification - that's their major shortcoming. They are an aerobic filter whether they are submerged or not (although much more effective when not). They are not porous, therefore whether they are being used in their intended wet/dry application or they are used submerged, they still don't offer a place for anaerobic bacteria to grow - thus no denitrification. They have their uses in aquarium filtration, but they're not the best filtration setup for a reef.
The vast majority of reefers today rely on a skimmer + strong circulation + live rock/sand for filtration. The fact that the hobby has headed in this direction is no accident...
FWIW