Aside from adjusting for the video delay produced by certain components (HD cable box, upscaling DVD player), the only sync issue I've encountered regularly is the HD feed from one local station - it's pretty much gone away now, but for the first year that I had HD they seemed unable to sync audio and video (the error showed up in both OTA broadcasts and over cable). The 990 itself hasn't caused any sync problems (it's just helped fix problems produced by other components' video processing delays).

I assume that the two subs you are connecting are equipped with XLR inputs. There are some splitter cables or devices available for XLR connections. This thread might be helpful - there are links to a splitter cable or two and a splitter box.