hooking up a subwoofer to a Mcintosh MA12000

You can use either output 1 (RCA) or output 2 (XLR) depending on your subwoofer inputs. If you want to hook the sub(s) up using speaker level, otherwise known as high-level inputs you'll have to ask McIntosh. If the integrated is truly balanced then you can't just go positive to positive and negative to negative. The ground would have to be attached to one of the grounds on the back of the integrated.

got it...and will the volume output match the speakers?

the sub is a Velodyne, digital drive series from a few years ago. If it works out i will upgrade to a JL Fathom. My speakers are Martin Logan ESL 13A's

The volume will be controlled by the MA12000. The only thing to be aware of, is in the future, when you buy your subs try to match the efficiency of the main speakers with the subs. If the sub is at 85% and the mains are at 95% as you go up in volume, you may have to increase the gain on the subs to match at higher SPL of the mains.  The bigger issue is setting back down, turning the volume down and the SUB is way to loud. It is a PITA for a lot of high efficiency horns trying to use standard HT and music subs. They never quite work the way they should..

sub is a Velodyne, digital drive series from a few years ago.

In that case come out of the RCAs. You'll need a Y cable to come out of the amp with one cable to the sub and one returning back into the amp for each channel.