Some HUs with only two sets of preouts have an option where the rear set is switchable to a subwoofer out.
If this isn't the case with yours then you'll still want to hook your sub amp to the rear preout and (assuming your HU is lacking internal crossovers) you'll need to use either the LP crossover in the amp itself, if so equipped, or an outboard crossover so you're not sending a full-range signal to your subs.