You need to set the height at which the antenna is going to be installed above ground level. It is not always possible to mount an antenna right at the top of a tower, so using the full tower height may not be appropriate.
LINKPlanner will warn you if you set an antenna height that is larger than the maximum height of the site. You can use the tower height to define the maximum height at the site. This can be configured in the network sites list.
If the antenna is installed lower than the height used in LINKPlanner then the link may not have the clearance expected during the planning.