While prolonged overheating can be bad for things in there, if it happens in short terms, I wouldn't worry TOO much. Perhaos find an app that will let you know internal temperatures, and if you think it's getting too hot, shut it down for a while. In other threads I've read, clearing the dalvik-cache seems to temporarily help as well, if you're rooted.
My phone generally heats up while on a long cjarge with its case on (I remove the case to let it breathe now), during long periods of playing graphic-intensive games or running programs that use a lot of my processor (I underclock things at times now, helps a bit), and in the car when using GPS (I'm in Texas, though...gonna happen.)
None of these things have gotten the phone as hot as I had to when I replaced the glass lens. Lacking a heat gun, I used my hair dryer on full blast to melt the adhesive. By the way...leave it to professionals. It worked out, but shattered glass stabbed me a few times. But during the process, I had to get it so hot it hurt a little to touch. Of course, the focal point if the heat was the glass, but I digress. I'm running the Jedi Master ROM, and the only tines the phone lags is when I start typing to fast for it to keep up. System, ui, all that still works pretty well. Well, except when I break it.
As long as it's not TOO hot, heat is going to happen. This is a fairly power-heavy device, so when it gets going, heat is a by-product. Just keeo a weather eye out and judge it by your situations. Youbshould be alrigyt.