O1S, The RTA feature on the PA+ is a tool to help you when setting up, just a tool. Eq'ing is entirely up to you.
Music is supposed to be clean and balanced, the purpose of an eq is to adjust down some thing that is to high or boost some thing that is too low, similarly if you tops are over coming you subs, turn down your tops and the bass will sound louder. There is a lot of fiddling around to get you system dialed in to a good balance. The venue has a lot to do with it also, obviously outdoors is a whole different ball game to indoors, thats where the PA+ wizard RTA comes in, to quickly measure the indoor room nodes and compensate for them with a relatively flat response, it is not the end all there, it will sound good but not great, that's where your ear and fine tuning comes in. There is so much to say about eq'ing, Id suggest some reading if your not sure.
Those Tubas are supposed to be really thumping, the build was great and you have the power. Before doing anything double check the voltage going to them at the rear of the amps and also at the end of the speaker cable run, it should be the same or very close.
One thing to mention is that our ears compensate overtime for sound levels, i.e if listening to loud music over time it will seem to get lower, its our body adapting. When tuning its good to take breaks and let the ears return to normal and then go again.
To measure the cabs response you will need a SPL meter which has c weighting and a tone sweep, or you could do it manually, with individual tones, 20hz, 30hz, 40hz up to your LP setting or say 100hz.
All enhancements on the PA+ should be off and eq set at zero across the sub freqs. Better yet google test tones and use your laptop to generate the tone, send it to the amp, adjust voltage at the amp output to 2.83v, move sub into a free space with at least 50ft of nothing around it, plat test tone and put spl meter 1 meter on a towel in front of the cabs mouth. This way you will be measuring only the cab and nothing else. For every tone you play measure the spl and right it down next to the freq played. After compare to SPL chart of cab posted here
http://billfitzmaurice.info/forum/viewforum.php?f=12
you can repeat test at 10m distance and 28.3v
Even this simple test is not the end all of test, its merely a reference. If the figures are close to the cabs spl chart all is well, if way off something might be amiss with the cab or driver and that where the fun starts, ask missile crisis .....