What hardware do I need if I need to frequently adjust the height and rotation of 2 Thunderbolt monitors?
Two 27" displays will (obviously) take up quite a bit of room. You'll probably want to look for a desk that has built-in mounting points for your VESA arms (or built-in VESA arms) so you don't have to hang the displays off the wall. (If you want to rotate the monitor, Apple's Thunderbolt displays don't have any built-in rotation ability, so you'll need an arm that does that, too. OS X's Displays preferences are where you'll go to set the rotation on the display.)

There are several different caddies for your MacBook (such as the Henge Docks) that will keep it out of the way of your displays.