Flying machine is a glitch that allows to freely fly in the air using 2 minecarts or a minecart and a box
To assemble a flying machine with minecarts place the first one on flat ground, stand behind it and place the other one perpendicular on top. Pull it slightly towards link to make the lower minecart tilt upwards, which is not always required but makes the liftoff more stable.
Then jump on the minecart stack, position link on the center of the top minecart and magnesis the lower minecart. Lift it slightly up and make sure, link always stays in the middle so adjust his position if necessary.
This works, because the game only checks if link is directly standing on the object that is lifted with magnesis, but by having a middle layer bypasses that check.
There's three degrees of control for the Flying Machine
Magnesis (D-Pad up & down): Controls the Flying Machine's acceleration. Holding up will make the minecart go forward. If you need to lift off in place (which is particularly useful for Box Machine), pull the minecart towards you with down as you are rising up. For normal Flying Machine, you can simply hold neither during the initial liftoff if you have enough space to do so.
Camera (Right Stick): This controls the lift of the Flying Machine as well as its course of direction. Gently tilt up on the right stick to rise up. While moving forward, rhythmically tap slightly down if you wish to descend with the Flying Machine in one piece (ex: All Dungeons Zora's Domain entry in ZDI's run). To turn, gently tilt left or right; if you wish to turn in place, this must be used in tandem with moving Link. Note: if you have the camera inverted, you need to adjust the directions accordingly
Link's Position (Left Stick): Link essentially acts as a stabilizer for the Flying Machine; in ideal conditions, he would be sitting in the middle with a perfectly stable minecart orientation. If the Flying Machine starts veering towards one direction, move Link gently towards that direction to even it out; as the Flying Machine centers, move Link back to the center.
written by PuppetMaster9
Tutorial video here.