Which one?
Do you have a model number for us?
I'm not an expert but I have used Audyssey and Paradigm's room correction for the sub. I will also post the disclaimer that I prefer my manual settings to anything Audyssey comes up with, although Paradigm's sub software did great. If you choose to use this software use the max # of measuring positions.
Turn on the TV and put the volume where you normally watch - then run the software (with the TV off!). But remember, the software isn't trying to find the "right" volume. It's trying to find out how various frequencies behave in your room and adjust accordingly. Once that's done it'll be "right" at whatever volume you choose.
Once the software is run there's a few things you can do if you like to tweak. If you have a meter you can double check the speaker's volumes. In addition, if you know you have difficulty hearing certain frequencies you can further boost the volume at those frequencies. That's all the fine tuning I would do though.
One exception is subwoofers - After I did my room EQ I had to fix the crossover. Apparently the software (in my case Audyssey) decided to crank the sub's volume down and pass only the deepest bass.
Once you have something that sounds acceptable to you let it sink in and adjust for a few days. If there's things that irritate you, then adjust further. If not, you are golden.
My last comment is on ambient noise. Try to turn off everything that emits sound intermittently like HVAC, dishwasher, kids ... as the software WILL take this noise into account but it can't tell it's something that comes and goes.
Hope this helps somewhat ...