Let's be clear here...
In Phantom or Naza GPS mode during the 1-2 min warm-up and initialization phase that occurs everytime you power up the a/c, two things are saved or recorded.
First is the direction or heading that the a/c is facing with it's magnetometer, this is for use with Course Lock (CL). The rear LEDs will rapidly flash green for a second or so once recording is complete or successful.
Next will be the Home Point which includes GPS X-Y coordinates and the current elevation (as measured by atmospheric pressure). This requires 6+ GPS satellites to be acquired first and the time it takes depends on local GPS 'receiveability conditions'. Progress can be monitired by the rear LEDs via a green-red LED flash pattern. Once again the rear LEDs will rapidly flash green for a second or so once recording is complete or successful.
This should be your normal take-off proceedure, wait for both sets of rapid green flashing LEDs.
After each of these things is stored the a/c in generally considered ready to fly.
Once airborne you can enable and disable CL as you wish.
You may also select CL before you take-off but that may not be adviseable as this is the time to check the 'health' of the a/c prior to flight with basic control inputs and CL could confuse the pilot.
Additionally the Course Lock heading can be reprogrammed in-flight via the S2 switch. Once the a/c is facing the new direction or heading you wish to store, move S2 from Off-to-CL-to-Off 3-5 times. Just as before, the rear LEDs will rapidly flash green for a second or so once recording is complete or successful.