AI transport helicopters will be landed by the AI where the AI transport helo routines decide, they will not follow waypoints. (These routines are there and used by the AI when it gets transport helos in a normal battle, it will decide the landing zone area for itself based on battle type, objective placement, and if it decides to drop onthe enemy rear zone to attack the gun line today etc)).
It is best to leave airmobile assault operations to the human player in a scenario, and never to the AI.
AI paradrops and gliders can be (and must be - it will not plot them for bombardment missions itself) programmed as part of the pre-game bombardment, the unloaded infantry will wander about towards the objectives - so OK for a scenario of say German (human) versus Allies in Normandy, or NZ versus Fallshirmjaeger in Crete, where random lost packets of paras cause problems for the defender as they pop up from unexpected places
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For helo operations - the AI will plot where it goes, so provide helo capable landing areas (open ground basically) near the objective clusters (and keep the objectives close by to avoid shotgun effects as the AI decides the LZ to use) and the AI will decide where it puts the desant LZ by itself. That will differ game by game. You will need to experiment with your scenario to find out what happens, over many test games.
Cheers
Andy