If you had the subwoofer adjust On and +4 before Audyssey, it likely ignores it during calibration process anyway. You can just now turn that off.
I'd leave the subwoofer trim as Audyssey set it, since it balances it with reference volume. Keep DEQ on, since it compensates for our lessened perception of bass as the volume decreases. DEQ adds about 2.2dB per -5 volume from 0 (reference). Most people listen around -10, which would result in a 4.4dB bump by DEQ...this also matches the general recommendation of increasing subwoofer +3 to +5 from people who manually bump the bass after calibration (and not use DEQ).