What you do with the throttle and brakes in the air actually affects the attitude of the bike; if you blip the throttle, it tends to bring the front wheel up, and if you let the gas off, or hit the back brake, it drops the front wheel. Gyroscopic action / torque, and all that, y'know.
So if the landing point is sloping away from you, having the front end down do both wheels hit at the same time is a good idea, but if it slopes up, having the front wheel up is good.
You can also use a bit of 'body english' before you hit the jump, and to adjust the attitude of the bike in the air too, to make sure the bike flies nicely, looks styley, etc. Of course, all this depends how long you're in the air - if you're only a few cm off the ground for a millisecond or three, it's irrelevant.
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