The cut-over frequency is supposed to define at which frequency the sound is diverted from the front speakers to the subwoofer. Ideally, you should set it at a point where the transition from the front speakers to the subwoofer sounds seamless or smooth. Normally, this frequency is 80Hz. If you have a way to generate a frequency sweep (and an RTA to go with it if possible, otherwise you'd have to rely on your ears), it would help you a lot in determing where the front speakers roll off and consequently where the subwoofer should come in. What you do not want is to have a "frequency hole" where the front speakers are not capable of playing the particular frequency anymore and the subwoofer hasn't cut in yet. When you generate a frequency sweep, the sound will fade towards the frequency hole and come back again.
The subwoofer level volume setting (if it has one) should also be set such that it is loud enough to enhance the low frequency effects but doesn't attract attention to itself.
Hope this helps. Enjoy!