I might actually go in a little different direction with respect to DEQ. First, how do your SB1000's sound with movies? Are you getting the bass support you want there? Second, have you raised the sub trim level from where Audyssey set it?
DEQ does add a bass boost, but many people don't like that particular feature as much for music. One thing that DEQ does is to boost the bass in all channels and not just for the sub channel. I can't answer specifically why your Ultra's seem to have more mid-bass than your subs, but there are a couple of things I would try.
First, I would turn off DEQ. (That will enable the tone controls which affect only your front speakers, if you want to selectively add some bass boost to those speakers.) Second, I would add some trim boost to your subs. Try not to get the trim over about -3, but if you started well in the negative range, that shouldn't be an issue. The subs should be able to play mid-bass much more effectively than your bookshelf speakers, but they may need a little trim boost to do it, since Audyssey originally set them to play at exactly the same volume as your other channels, and we don't hear bass frequencies as well. A +3 to +6db boost is common. Third, experiment again with both 60 and 80Hz crossovers, and if necessary, add just a little bass boost to the Ultras using the tone control. You are essentially seasoning to taste.
The Reference Level Offset is simply changing the amount of boost that DEQ applies, by changing the point at which the boost occurs relative to Reference, which is a master volume of 0.0. You can try the different RLO settings, but I would also turn DEQ off and play with the sub trim level, as suggested above, to get a good baseline. None of these changes will affect the actual EQ that Audyssey performed.
Regards,
Mike