For the ceiling speakers, room correction will work as normal (many people already have surrounds placed high up on the side walls or the ceiling).

For Atmos-enabled upward-firing speakers, there will have to be a high frequency squiggle (two peaks and a notch) inserted into the target curve. This squiggle in the frequency response is part of Dolby Elevation processing and fools our human heariing into perceiving those sounds as coming from above.

http://www.avsforum.com/forum/attachment.php?attachmentid=256866&d=1410403980

However, psychoacoustic notches cannot fool a microphone, so room correction systems have to come up with a way to figure out where the virtual speaker is (since it is difficult to measure a virtual image). Audyssey, for example, will be doing this using simple trigonometry, assuming typical listener and ceiling height. So if a height module is roughly at ear level 8 feet away from you, the virtual speaker will be about 11.3 feet away.

http://www.avsforum.com/forum/attachment.php?attachmentid=221778&d=1408599474