Why not use a "Y" cable to connect both right and left speakers to the sound card?
REW outputs a mono line level signal - you do use a splitter when connecting it to the Left and Right CD inputs of your receiver.
If you click on the "Room EQ Wizard (REW) Information Index" sticky thread at the top, you will then see links, guides, tips, etc. Under "Guides", click on "REW Connection and Cabling Basics".
There should be a connection schematic with the following explanation.
The line-out right channel of the soundcard connects to the receivers (or processors) AUX or CD input. It's a good idea to use a Y-splitter at the receiver to feed both the left and right channels, so both mains speakers may be checked along with the subwoofer.
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my sub is connected to both speaker amplifier outputs
I'm assuming your receiver does not have a dedicated sub-out RCA jack and you have the sub connected to the main speaker level outputs. Thats fine. You can lift a wire from each main speaker to isolate the sub and use REW to see how it interacts with the room. Or you can power down the sub and measure the mains response without it. Or you can measure it all together.
Whatever you do, I hope your results are better than mine. Two things I have not successfully accomplished - Growing green grass in the front yard and getting a half way decent bass response. (Other things I haven't done, but those two just rub a bit!)