Yes, its generally a bad thing. Your sub isn't playing a discrete channel like it would be in a 5.1 or 7.1 soundtrack, so its bass is overlapping with your main speakers. In most rooms that will cause cancellation of bass frequencies and actually reduce the amount of bass. If you have a properly calibrated setup where you've adjusted phase, distance, SPL, etc. then you could run your fronts as Large. Otherwise I'd recommend running them as small.
Like I mentioned before, set your sub's crossover as high as it can go on the sub itself and set it to 80Hz on your receiver.