OK Essay no 2
What sort of sub / main speakers are you using?
What is the problem with the sound? Detached?
How big is the room? Shape and dimensions?
Above method should work for both 2 channel and surround. As the speaker configuration is different for the two though this can affect where best position for the sub is. If your surround speakers are small enough though (and the vast majority are) you'll probably find that the best location for 2 channel is the same as for surround.
A lot of people seem to prefer different settings for music and surround duties.
There are all kinds of nice touches that could be built into the digital stages of the LFE channels which I understand are now being implemented to some degree. Read that section of the Onkyo manual. If the Onkyo gives you presets for how the LFE behaves so much the better. Do you get a mic and an auto calibration utility?
If so use it.
Ny Yamaha is 5 years old and gives no scope for control other than a level adjustment.
Try to find the low frequency at which your main speakers are -3dB and match the Onkyo to that and the sub to max frequency. Adjust the sub volume to blend in with the mains. Then see if you have any control over the slope on the Onkyo (look for things like -12dB per octave, 2nd order, Butterworth, Linkwitz Riley etc in the LFE parameters set up). You may well not be offered that flexibility though. If you have it experiment using test tones around the crossover frequency to try to get the volume as level as possible. Look as well for Parametric EQ on the Onkyo (again, if it has it). Use this as the next stage in tinkering for a flat response with test tones.
If you have a dip in responce above your crossover frequency on the Onkyo, increase the crossover to a higher setting to try to smooth this out. If the response peaks above the Onkyo crossover frequency try lowering it.
You can later lower the subs own crossover frequency to try to cure peaks above the Onkyo crossover frequency.
Again, if you have room response problems, there's not much that you can do with tweaking the above the cure it.
Once you've got your system as flat as possible you can use that as a starting point to get the bass sound how you actually like it. If you do the above though you'll have a good idea what to change to make it sound the way you like it.
I've probably overcomplicated this. If you just accept the default settings on the Onkyo and experiment with level, phase and crossover you should find something that's nearly acceptable.
That's what most people do.
If you mostly listen to stereo rather than surround though, you could always experiment with using front pre outs or front high level outs to feed the sub its signal.
There I go complicating it again.
Read, experiment, relax with music or movies and a cup of tea and enjoy.