Design of cavity filter
When designing coupled resonator filters I have always used tables of k and q from "Handbook of Filter Synthesis" by Zverev and scaled them for centre frequency, bandwidth and impedance. There's probably an online resource these days. 
To determine the loaded Q of a resonator in isolation, you can look at the bandwidth at a given return loss figure. There is a relationship between Q and, say, 10 dB return loss bandwidth but I can't remember what the numbers are. This only works if matching is close at the centre frequency. 
For tuning a physical filter, Dishal's method works well. I'm not sure how well that can be applied to a simulation.