If you didn't get a manual for your Bose system you can download it here: http://worldwide.bose.com/productsupport/assets/pdf/guides/acoustimass/en/owg_en_am15_series2_am16_series1.pdf
As indicated there, connect the LFE input RCA to the Subwoofer OUT on the back of the receiver. That provides a direct connection for LFE (low frequency effects) in .1 soundtracks if you set the speakers to "large" as indicated. It appears there are two fine tuning knobs, one for global "Bass" level and then an "LFE" knob for the .1 channel directly (although you probably don't need to adjust this after calibrating).
All that said, the Bose system is generally regarded to be inferior for true HT action. If this is a semi-serious setup, at the very minimum you should consider adding a REAL subwoofer to supplement the bass output of the wimpy Bose bass module. In this case, you would not hook up the LFE connection on the Bose at all, instead connecting the dedicated subwoofer to the Sub OUT on the back of the receiver and then just letting the Bose module supplement the bass of the little cubes. In this context you would override the manual's suggestion and set all speakers to "small" with a 60-80Hz crossover so that the real subwoofer gets not only the LFE track, but also redirected bass from the other 5 channels.