There are essentially four 2-1 options for your XT660R. Here they are listed roughly in order of cost:
MTC - Cheapest option, using the stock low headers and a link pipe to allow a single can (and can be purchased with a forum discount):
http://www.xt660.com/showthread.php?t=22657
Creptus - Custom built high level headers and single can:
http://www.xt660.com/showthread.php?t=23542
http://www.creptus.cz/index.php/en/
Metal Mule (made by Scorpion) - High level headers and single can:
http://metalmule.com/by-product/exhaust-systems/yamaha-xt660r-xt660x-replacement-exhaust-system.html
OTR - High level headers and single can (the headers can also be bought separately so you can fit a choice of cans, or source one from elsewhere):
http://www.off-the-road.de/en/XT-660R-X/Exhausts/OTR-SR-2in1-system-e-marked.html
http://www.off-the-road.de/en/XT-660R-X/Exhausts/OTR-2in1-headpipe-system-XT-660.html