Omega,
I'd just keep your center set to large. I have a CLR 3000 in my HT, and setting it to large is the best way to run it in my set up, the sub in the center channel (even in the larger CLR 3000) isn't designed to add deep thumping bass; it's purpose is to simply make the speaker a true full range speaker, so just keep the center channel signal going to it full range, don't send the LFE to it. Actually in your set up, I'd probably just run all 3 front speakers as full range and take the splitter & LFE cables out, that's what DefTech suggests for such a set up.
-Brad