It won't matter at all. For nearly all integrateds, all channels are driven off a single power section, so the less you drive off of it, the more power you have available for whatever is connected to it. Having input to a second channel makes no difference as well, if nothing is connected to the output.
If this is a NEW stereo amp, I'd use each of the channels for a while, to break in the electronics on both sides. Long term, I might swap from side to side once in a great while.