Commanding:
First, dinnae just jump in and and start changing waypoints. Some people may have an operation in the works and the sudden course change of thier flat top could be verra detrimental to it (not to mention you if they ever find you

).
Plan your route. Think about where the best point to start launching your kites is and make sure you've got a nice long stretch with no turns there. It's VERRA hard to launch/land if the boat is turning.
Then think about getting your 8" guns to bear. Make sure you get the fleet close enough to the target, but far enough out that it's not in too much danger

Recovering your kites, same as launching, you need a steady course.
It's also good form to warn folks when you're making a change to the planned route, so they dinnae try to drop in the slot when the deck is about to turn (good way to ruin a day

)
Waypoints:
Dinnae set a pattern too close. Constant turning isn't good for launching/landing aircraft.
Patrol vs Looping:
Patrol goes to the last set waypoint then begins a back and forth patrol. Looping does just that, it connects the last set waypoint to the current position when the points are set and creates a big loop. If you're setting waypoint and get a "Waypoint touches land" message this is probably why, the leg that closes the loop.
Flying to/from flattops:
Check the map and look at the fleet's plotted course. You can choose the specific fleet you want to look at (if there are 2 or more TGCs operating together) by clicking the SHIPS button the clipboard and selecting the TaskGroup/CV you're wanting to land on. If you see she's about to make a turn, orbit in the pattern until after the turn, then land. Or, for launching, sit in the hanger and wait til the turn is made.