I have my HT set-up and 2.1 channel set-up in the same room. I have a Velodyne SPL 1500R subwoofer that I was using for the 2 channel part of my system. I took a look at the back of the Velodyne amp and there is a 2 channel inputs and one of the inputs also said LFE only. I took a male RCA to 2 female RCA Y adapter and plugged it into the LFE input jack.
My 2.1 channel preamp doesn't have a subwoofer output just another pair of outputs. My HT Pre Pro has an LFE output. One channel from my 2.1 channel preamp and the HT LFE output is plugged into the Y adapter.
If this doesn't make sense you can e-mail me and I'll send you a picture of the set-up.
Now I was able to use the same subwoofer in both systems BUT it was at different times like others have said above. Another issue I ran into was that I had to keep adjusting the volume and equalization on the sub to match both systems. The Velodyne doesn't have the ability to store 2 separate equalization/volume settings. I have some flexibility with my HT Pre/Pro so I can try to figure something out with the sub.
Good luck with your search.