Actually Reshiram and Zekrom have much better catch rates than normal legendaries (45 as opposed to 3). So they should be fairly easy. I caught mine in a Quick Ball (thrown on the first turn), but otherwise just get their HP down low as usual and try Ultra Balls.
You should save a Masterball for Thundurus/Tornadus who is roaming and generally annoying to catch. You can get a second Masterball when you have done 50 trades over the GTS.