Sounds like what I did... HU equalizer controls my subs bass, withought affecting my mid speaker bass (too much). Here's what I did.....
Removed panel to get to the amp.
Tap into right rear and left rear speaker wires AFTER the amp.
Run these leads to your high level inputs on subs amp.
Connect rest of amp (power, switch, and sub) as usual.
Now for your HU...
BEFORE sub is turned on, adjust your HU equalizers bass to the range that you want your mid speakers to perform.
Now turn on sub and amp, adjust your amps input level and gain to desired settings.
Viola! You're done!
This setting will not let you control ONLY your sub with the HU equalizer, but you will find that turning up the bass with the equalizer has BIG affects on the sub, but minimal affects on the mid range speakers. Hope this helps.
just as a template, I set my equalizers bass to -2, adjusted my amps sub to a balanced level of in-cabin bass. When I turn my bass up to +2, or even just zero, my sub hits MUCH harder... yet is hardly noticeable on my mid range speakers.