That's what I'm doing at the moment. I have a pair of speakers biamped with a 5 channel power amp, with the full blessing of the manufacturer. You simply don't use what you don't need. No need to cap anything.
Also, if the multichannel amp uses a single power supply, particularly if it is not especially large, the amp might actually sound better the fewer channels you use. You would have fewer channels drawing the available power from the common power supply.
Also, if the multichannel amp uses a single power supply, particularly if it is not especially large, the amp might actually sound better the fewer channels you use. You would have fewer channels drawing the available power from the common power supply.