There are some guides on-line regarding sub placement but, of course, depends on where you can place in your room.
I keep my subs out of corner - not a fan of corner loading.
Some recommended placements for duals include opposite "corners" (eg Left Front, Right Rear or vice-versa), 1/4 way in on either side of front wall (this is approximately where I have mine, although more like an 1/8 due to space), middle of front/rear walls, middle of side walls.
Drivers don't necessarily have to point at MLP. Play around with different orientations to see how that impacts response. You can even point towards the wall.
As to gain matching, this is what I did with my dual Rythmik E15's, miniDSP 2x4 HD, and REW.
* Set sub volume (or gain, depending on how it's labeled) to 12 o'clock.
* Set AVR volume to -20 (although I don't think it matters where the volume is).
* Set AVR sub crossover (LPF) to max (in my case 250)
* Turn off other parameters in AVR (eg, Cross-overs to flat, distances to 0 (except whichever speaker you are using for timing reference - I chose the Center - input the measured distance), trims to 0, clear all EQ filters that may have been uploaded into the AVR). Use the speaker profile (if you have multiple) that's set this way for REW.
* set up controls on sub amp as per recommendations (eg, defeat any PEQ, max cross-hover, low damping, max extension (in my case 14 hz), rumble filter off, etc.
* Make sure the mini-DSP is set up (eg, no PEQ, no trim, no cross-overs, etc.)
* Set up REW preferences and Windows (or Mac) as per on-line guide (AustinJerry on AVS has an awesome guide).
* Place mic, pointing to ceiling, as close to sub 1 driver as possible. I used 5" from the lowest point of the driver.
* Turn on sub you are measuring in miniDSP, others are off.
* Use pink noise from either AVR or REW to measure sub 1 output. Record.
* Move mic to sub 2, same distance.
* Turn on sub 2 in miniDSP, others off.
* Measure sub 2 output. Record.
* Decrease gain in miniDSP output for sub that reads higher. eg, if sub 1 is 105 DB and sub 2 is 110 DB, apply -5 gain to sub 2 output.
* Repeat each sub, if you want, to confirm measurements.
* Turn on both subs.
* Voila, you have just gain matched your subs (w/o having to move them to a certain position in the room). I believe it's Ep26 (or 26.1) from HomeTheaterGurus where he explains gain matching. This method is explained towards the end of the video. He says there may still be some room boundary effects, but likely negligible (IMO). Much easier than lugging heavy subs back and forth.
* Now you can move to the next step (aligning).
* Measure each sub independently in REW at your MLP.
* Measure both together.
* Add delay in output(s) of sub(s) (or you may need to invert one if behind you) to get the best response of the summed sums (eg, the curve above both individual measurements by ~6 DB if possible. May not have that much output across the frequency response. In my case, there was a spot around 75 HZ where the summed was a bit lower than one of the individual measurements by about 3 db. I could never get it above both playing with delays w/o hurting other parts of the graph. That was fixed with EQing.