Splitting is fine if the Subs being split are symmetrical in the room and equidistant from the MLP.
This, of course, is dependent on the AVR actually managing the 2 SubOuts independently (as there are AVRs out there that have 2 Sub Outs but are really just an internal splitter (you can tell which your machine is by whether you can set individual Level/Trim and Distance/Delay for each output)).
Beyond that, if you really want absolute control, this is where the MiniDSP 2x4 comes into play. Using REW and a measurment mic like the U-Mik 1, you can take very detailed measurements of how each sub is performing and dial them in with their own Distance/Delay, manual EQ, etc.
Combining the MiniDSP and your own Room Correction, you should be able to suitably micro-manage (to the fullest of any potential OCD) your way to a very clean and flat FR, or build your own house curve.
