I hear ya. Haven't done anything yet. I know it's going to take an entire morning or afternoon if I do and I'm not exactly chomping at the bit to go through all that effort to find out (most likely) that it was better the way it was.
To address what you're telling me, my 2 subs are already level matched. After that they're eq'd together. The mini is what I'd use to apply filters separately. Get the towers right, then get the subs right, then do them all together. Say, channel 3 for both subs and channel 4 for both towers (bass section only).
I'm stubbornly sticking to this idea because
@gene popped in here and said he's gotten the best results with this configuration. I'm always game for "the best". I'm not always game for a lot of work with the promise of (maybe) poorer results. I'm still considering. Plus I'm a little gun-shy after blowing up my 1400 watt amplifier.
That was 100% user error on my part. IF I do this the jumpers come off first before I touch anything else.