The high pass for the mains and center on my Onkyo only go down to 60 Hz, so I set it there. My mains are good for 40 Hz. (Klipsch KG-5/RC-35)
My reasoning was that you didn't want to set a six pole filter to the frequency where the response was already 3-6 dB down. These filters should have a pretty steep cutoff.
At 60 Hz, my mains are still pretty flat, so it seemed like a good crossover. I set the low pass on the sub to around 65-70 Hz. I weanted a little overlap and that seemed to give the flattest response.
I also experimented with full range on the amp and 100 Hz cutoff on the sub. The results were too boomy for my taste. I also tried the double bass setting on the amp, and that was WAY over the top.
The bottom line is that you need to do what sounds best to you. I lived for years without a sub and was happy with the sound. I only went there because I wanted a little more emphasis on effects for action movies. Even there, it is only important to punch up the lowest frequencies, thus setting the crossovers as low as I did.
NONE of this is going to apply to the typical HT user who has a satellite/sub setup. I have a Denon HTIB in my bedroom, and there I have the sats running full range and the sub set around 110 Hz and cranked up fairly high.
Bottom line is that my setup probably isn't going to help you much. You need to set it for what feels good to you. I always go ahead and formally set stuff up using the guidelines. I write the settings down and then over time will tweek stuff based on what I am listening to. Eventually, I get to something that works for me, or stuff is reallyscrewed up. If it is all messed up, I have the original settings written down so i can fall back to them. When I get to something I am satisfied with, I write that down as well.
FWIW, I am still fiddling with the sub, as I have only had it a couple of months. Right now, I am starting to think I need to have a couple of settings. What works for action movies is way too boomy for music. Romanitc comedies are somewhere in between, but probably closer to music settings.
I kind of wish I had picked a sub with remote, so I could set up presets on my Harmony. I am thinking about disabling the sub and making the mains go full range when I select music now.