Your amplifier is a 4-channel amplifier. For that reason, you should just connect one speaker per channel. You should make sure that your speakers are on matched pairs of channels.
Most 4-channel amps are labeled with a front pair (left and right) and a rear pair (also left and right). You need to make sure, for instance, that you 6x9's are both on the front pair (one left, one right) and that the 2 subs are both on the rear pair (one left, one right). This will provide you the most stable configuration for the amp and will allow you the best control for crossover frequencies.
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