I assume you have the LOC tapped into the outputs at the back of the headunit. The Bose headunits output close to a line-level signal, so if you're not getting enough juice at your sub's amp, then the LOC is padding down the signal too much.
How is your current LOC physically connected to the wiring? Did you use wire taps, or did you cut and splice the wiring? What I would do is find a set of RCA cables with female connectors on the ends, then cut the cables about 6 inches from the RCA connectors, strip the sheathing back and tap the wires to the wiring harness. You could solder them, but it's not critical to; just make sure that the connection is solid. I'd use female-connector cables so that you could easily disconnect your existing RCA cables (that go from behind the HU to the sub) if you needed to.
With the non-Bose systems, it's actually better to tap your LOC to the front speaker outputs, not the rears. People have found (inluding myself) that the non-Bose headunit does some frequency attenuation on the rear channels based on volume...so the more you turn the volume up, the worse your sub will sound. When I moved my LOC from the rear outputs to the fronts, my BassLink sounded much better.