Rick, after you run the first sweep from the primary seat, instead of going onto location 2, there is an option to view your results upto that point. You can then see what it did to your sub levels. If they are set way to low, say -10dB, you can then lower the gain on the sub a little, and rerun your first sweep. Once I find a setting I am happy with, I continue on complete my other 7 locations.
One thing people don't know, is the 5-10 seconds after each speaker finishes the chirp noise, when it is silent, the mic is still measuring the silence of the room, so it is important to keep things very quiet until it is time to move the mic to each location.