It's perfectly fine to swap the left and right speakers if having them that way works better.  It wouldn't affect the sound quality; it would only affect the stereo image (the left channel being on the right and vice versa), which you can easily fix by using an RCA cable and switch the left and right plugs.

If you're using speakers like the A2+s or the HD3 via USB or the HD6s via optical, there wouldn't be a way to swap the left and right channels in your operating system's sound settings or through your software.