Hey Carr-Murell,
In order to set up carrier take-offs and landings within the FMB. The carrier must be set as the target.
Place your aircraft next to the carrier, not on it, and click take-off in the waypoints section. If there is a regular runway nearby the aircraft will automatically move to that. Just drag the aircraft back next to the carrier and click set target. Put the green target circle on the carrier you wish to take-off from. For landings do the same with the carrier as the target.
Good luck in your mission building.
Tip