I set everything independently ( sub, tower, interior) then combine and see how it sounds, I then do some final tweaking.
You need to set your gains properly first. Haev you done this?
What eq are you running? Does it control both your interior and tower or each independently? or just one?
I typically start with my HU setting then work my way back. Mine are typically zeroed out or in the negatives ( treb/bass). I run the treble down on my wetsounds setup. Also IMO turn the highest frequency on yoru eq all the way down (for the wetsounds)