1) Let me clear up some confusion here. There is nothing wrong with using the set at boot option. Just leave it unchecked until you know your phone is stable. After that, check away.
2) Profiles should not be affected by unchecking "set at boot". All that does is set the main min/max every time your phone starts. Profiles still run as long as they are enabled.
3) If your phone is running fine without overclocking, and you don't see a difference, don't bother. You might get a slight bump in quadrant scores, but who really cares about those. Ultimately, if you can't tell the difference, all you'll be doing is draining the battery faster.