There's no problem with bi-wiring downstream of the sub. I think you could do either - add another set of speaker cables from the left and right channels to the sub, or move the speaker cables from the amp to the sub and add a pair of cables from the left and right amp outputs to the sub. The first option may be the most convenient if the sub's not going to be located near the equipment rack (less running back and forth with speaker wire), while the second option lets the sub's crossover work with both the signal used by the and the signals going to the speakers.