It has been a while since I dealt with MultEQ. What I did with my subs is just use an SPL meter to manually set the sub output volume to around 78dB. That way, I could just run Audyssey once instead of having to tweak the sub then run again. If your sub doesn't have its own gain adjustment then you are stuck with Direct Mode. I don't think Direct Mode allows adjustment of the cutoff frequency.
Your sub should be EQed as long is it is showing up correctly in the speaker configuration menu. There should be a menu option to check your Audyssey settings. Speaker Setup should be where you can change the gain on your sub and speakers.
I'm currently using Audyssey MultEQ XT32 with SubEQ which allows full control over the subs without the need for an SPL meter.
Denon AVR X7200WA, Emotiva XPR-5, Emotiva XPA-7, Sony XBR 75" 850C, Oppo BDP-103D, Roku 4.
DefTech BP7000SC (L/R), CLR3000 (C), SM55 (FH), UIW BPZ/A (SB), UIW 75 (TM).
JBL L7 (Sur), EoSone RSR 350 (RH).
PC 2.1 setup. Emotiva Stealth 6, SVS SB2000 sub, Emotiva DC-1 DAC.