I believe Brian designed the sub that way, to both provide the high pass option to the satellite speakers, and to also have the option of driving the sub with a mono signal or a stereo signal. So, you can run one channel to each woofer, independently to the other, for stereo playback. Or with jumpers, run the same signal to both woofers, for mono playback.
If I wanted to use the high pass feature, I'd use that input specific input box, for a cleaner, direct connection. But, electrically, I don't think it would make a difference. Either box should feed the the output connection.
As to the driver impedance, I'm not sure? Better to measure them first, to confirm. Still, I'd guess both were 8 Ohm drivers, for a parallel 4 Ohm load.
Good luck.