Are you two front placed symmetrically and your two rear placed symmetrically in the room? If they are, then Audyssey will time align them properly if you use sub 1 output to both front subs and sub 2 output to the two rear subs. They are not placed symmetrically, then you'd benefit from the miniDSP. However... sometimes having the timing slightly off from one sub to another can actually improve the response and fix issues. On a previous setup we moved my front subs 5ft farther away, which shortened the timing, and it smoothed out the response very nicely... and no one could tell the timing was off... as it's typically not noticeable enough to matter.
The miniDSP 2x4 would be fine... and you would want the Bass Management module, which would allow timing, levels and give you 10 parametric eq bands for each channel.
AustinJerry wrote a manual on time aligning subs with his miniDSP.... very helpful.
https://www.dropbox.com/s/w7jmpozner6muzw/MiniDSP 2x4 Set-Up Guide Latest Version.pdf