The sub should have two sets of speaker terminals on to connect the amp to and the other to connect from the sub to the speakers, so the sub sits inbetween the amp and the speakers 'in line'. The sub contains a crossover which will filter the low bass and then pass the mid and high end on to the speakers for them to do their stuff. The idea is that the two integrate. As bass is 'non directional' (not strictly true but it is LESS directional than other frequencies) then the fact the bass isn't over two speakers isn't too important.
The LF RCA ports you can see are for connecting an AV amp to so the sub can deal with the LFE (low freq effects) which are flagged up in a 5.1 soundtrack as specifically for the sub, a stereo amp can't do this, hence the crossover in the sub.
Hope that helps
MB