To use the fly, activate it with the right button, move around to where you need to go, and then press SPACEBAR and it will put you on the ground or whatever surface is right below you, including rooftops and other inaccessible places. AFTER you press the spacebar, THEN you can deactivate the fly mode and your character will have actually moved to that new place. Great for sneaking up behind wolves, placing your character, pulling out the gun and then BANG! Execution style.
EDIT: just be careful; animals will still see you again once you hit Spacebar, so if you set down right in front of them, even though you haven't disabled fly mode yet, they might still attack you.