There are several approaches, and what works best sometimes depends on luck, and whether you have identical model SWs or two different models:
1. Optimize location and EQ response for just one. Optimize location for just the other, and see if the EQ response works well. If not, consider doing EQ/response for the second, and find a new location for the first. Then measure for both and tweak.
2. Optimize location for first one, then add the second. Adjust the location of the second for optimal smooth room response. If you have a symmetrical room, the position will probably be symmetrical. Then EQ for the combined response.
3. If the subs are identical, you might want to consider co-location (stacked or whatever) for maximum SPL - but your room response will not likely be as even for the seating positions. So find the best location for just one, put the second one one top, and adjust EQ for frequency response.
I got lucky: the optimal position for one was not the same for two (symmetrical positions) when I added my second (identical) SW, but it turned out by placing the SWs where I wanted them for aesthetic reasons was also a great place for getting a very flat FR - or a well-behaved house curve (which is what I am using now, mostly).
Are your SWs two of the same, or are you mixing models?
shinksma