a glass cage? can you be more descriptive as to why a rock under the water bottle wouldn't work there?
as for you original question, yes you can cut their toenails but you have to be careful not to cut too far (or into the "quick"). make sure you only get the curvy bit of white at the tip. mind you this can be a real pain and make sure that you don't have any plans for the next hour for each rat that you do. it can easily take that long with a squirmy rat. if you do hit the quick however don't panic. it'll sting the same as when you rip a finger nail too far back but it won't kill the rat, it'll bleed a lot but a finger is still a far ways away from the heart. hold and apply gentle pressure to the cut tip until the bleeding stops. a way to get a rat to stop squirming a bit (for some rats) is to feed them treats to keep them occupied. all this makes me very thankful for the stone in my cage, works their nails down and no fighting with them on my part to get them that way! i love my stone. *grins happily*