What kind of receiver do you have?
If it includes room equalization software (Audyssey, YPAO, MCACC, etc), when you run the calibration it'll try to compensate for where the speakers are located relative to the primary listening position. Of course, it'll do a better job if they're at an optimal location to begin with.
Have you considered a 7.1 speaker configuration (if your receiver supports it) ?
In that case, you might consider putting speakers in both of the locations you mention.