It took me about an hour and a half today, but I've gotten everything pretty much how I want it for awhile. I had really tame the subwoofers down in order to get everything flat. They still run a little hot, but they were a good 10db higher than everything else during the measurements sweeps at first. If I run the level calibration on the Onkyo the sub channel 1 and 2 now read 65db when everything else reads 75. Needless to say that when you put all the 3 subs I currently have running together they're pretty potent.
The next step is to slowly but surely start getting EQ to the rest of the system. I'm still trying to decide if I want to use something like the MiniDSP Open DRC or to just get something like the 10X10.