You can land helicopters on the two helipads of your helicopter base. These Helipads are standard in a helicopter base:
Another possibility is to build a helipad in the tank factory of your normal base station. You can also land helicopters here:
First mark your helicopters and then right click on the helipad. Thereupon the helicopters fly towards the helipad and land afterwards.
A group of maximum 25 helicopters can land on one helipad.
The advantage: While your helicopters have landed, they cannot be shot down by enemies. Only when your last base defense missile launcher has been destroyed by the enemy, your helicopters will automatically take off.