The bass and treble effects are still viable with DEQ on, you just can't adjust them. If you want to make any adjustments to the bass and treble to use with DEQ then just turn DEQ off, make your tone adjustments and then turn DEQ back on. The adjustments last made with the tone control is still active with DEQ engaged.
I don't believe this is actually correct. Dynamic EQ defeats the tone controls completely.
We tested this last year with '09 models; put on some music and turn Dyn EQ off, adjust the tone controls to the opposite extremes (e.g. bass +6 and treble -6), turn Dyn EQ back on..... then turn it off and swap extremes, turn Dyn EQ back on. You should be able to hear a massive difference between the two scenarios (12dB delta between the extremes), but they will sound identical with Dyn EQ engaged.
The only way to really impact the "tone" with Dyn. EQ engaged AFAIK is:
treble -> if you want a little more, switch to Audyssey FLAT
bass -> tweak the subwoofer channel volume, or better yet the Dyn. EQ reference offset (to tone it down)