Your Bose system should sound just fine; but in mine and others experiences subwoofers can play hell with turntables. You may not have any issues, depending on placement, your chosen listening volume, and type of music, etc. If you have problems (for instance I was getting a lot feedback from mine) you can try removing the dust cover entirely while listening. And a thick rubber or foam mat under the tt wont hurt either. In the end, I just set up a vinyl only system in my bedroom and let the home theatre be just that.
Good luck and I hope you're enjoying the vinyl!
Are we there yet? No, never there yet. Keep it rollin', we're paid by the mile.