I have two 12" subs, and an 18". To get really good response in my room I did the following. I completely agree that getting rid of peaks is easy, so focus on reducing dips first.
This process might not be perfect for you, but my recommendation is to start with position of the subs. Next, tweak phase and delay. Then apply EQ. You can do things like I did with filters and EQ on specific outputs, but it's not necessary.
The very long version of what I did:
Baseline
First, I disabled all EQ on the miniDSP to start with a clean slate. I ran sweeps in REW with everything on and no correction/EQ for a true baseline. I then ran Audyssey on my receiver, and used the app to stop Audyssey EQ on the subwoofers.
Correct for dips with Phase and Delay
I then ran sweeps with only one sub enabled at a time. In MiniDSP I adjusted phase (inverted or not), and adjusted the delay 1ms at a time, until I found the best response for each sub. You can then run them all enabled when you're done to confirm the response looks much better than your baseline. Note: I used this to get the most flat response, not the biggest peaks at random frequencies.
This made an enormous difference, getting me close to a relatively flat response without any EQ. I can't stress enough that t
his made a far bigger difference than EQ. In fact, results after this step had been drastically better than just using Audyssey or just using EQ in MiniDSP (I know, because I tried that first and wasn't happy).
Protect my little guys
Next I put a high pass filter on the 12" subs with a steep roll off under 20Hz. The 18" sub can handle all of that.
Reduce the Peaks
Because the 18" sub had a significant bump in mid-bass, I used REW's EQ generation tool to flatten it. Note that I did this before global EQ across all subs because it was the one major problem and it was isolated to one subwoofer. So I took sweeps of only that sub again, used REW to generate a filter file, and applied it to this sub's output. This is an EQ on that specific sub only, not the input signal to the MiniDSP.
From here I followed the typical REW auto-EQ process that I just used on the 18" sub:
https://www.minidsp.com/applications/auto-eq-with-rew
I had to play with the Filters and target curve to get what I wanted. I added a couple manual filters because the purely auto EQ still left one significant peak that looked higher than I wanted, but talking true fine tuning at this point.
Hope that helps.
Edit: my results from the above steps (I got it a bit better, smoothing 70-90Hz, with the last round of EQ adjustments but forgot to save the last runs in REW.)