A 2-channel amp means it has two outputs to connect speakers and it's not just limited to a speaker per channel.
You'd be better off with a 1 channel (mono amp).
Add up the RMS power handling of both subs and get a mono amp that matches @ 2 ohm (only If the subs are single coil 4 ohm) and wire the subs parallel - http://i81.photobucket.com/albums/j230/sparky3489/PARALLEL.jpg
More info here http://spkrbox1.spaces.live.com
