Great, thanks all for the advice. I've finally gotten the hang of this and figured out it had to do with the crossover settings and the speakers being set to large (as well as not having the initial gains set right on the sub during YPAO calibration). I have the polk RTi A3's for the front, the A6 for the center and the Rythmik LV12R which is a replacement for their FV12
So is it sounding good now?
If not and if reading the articles in the link BSA provided didn't help here's a quick rundown.
1) Double check that all your wiring is correct and securely connected including speaker wire polarity.
2) Turn off all EQ on the sub if so equipped.
3) Disable the crossover on the subs amp and adjust the volume knob to desired starting point. (refer to your manuals) If the sub dose not have a switch to disable the crossover then just turn the knob all the way up to the highest setting.
4) Manually set your receivers distances for all your speakers.
5) Manually set all your receivers speaker sizes to small.
6) Manually set your receivers crossover setting to 80hz.
7) Manually set all speaker trim levels to zero.
8) Manually set your receivers phase setting to normal.
9) If your receiver has a setting for base output, set it to output to the sub only (SWFR), not both or front. (these labels might be different on your Yamaha but that's how they are named in mine)
10) Turn off or zero out all settings for EQ and tone controls.
11) Save this setup (at least for the time being) It is the starting point that most of us here begin with.
12) If your receiver will let you run YPAO so it only adjusts the volume level and EQ of each speaker with out changing size, crossover and distance then do so and see how it sounds.
13) Tweak to your liking. Getting a SPL meter is the next step if you don't have one. Manually setting speaker level is more accurate in most cases.
All of this wont take you long. Remember, these are starting points. You might not need to change them you might need to change all of them. Most of us change very little from the small / 80 hz settings though. YMMV. (Speaker trim settings will change)
If you have questions...ask!
There are many here who are very helpful...some are even patient!