6 channel amp in a 5 speaker config

I'm using an amp that uses 3 pairs. One pair will be for the mains, 1 pair for the rears and then the next pair for the center. The manual shows the center and the sub being on the same pair to utilize both outputs but I don't have a sub.
Is it ok to just run one channel on this pair or does that create some sort of problem for the amp? If I have to I figure I could bi-amp the center channel and utilize both outputs on this pair.