If memory serves, you're supposed to create an AI (non-player) squadron, assign them the plane type, payload, mission type they'll perform, and then create waypoints for them and the action assigned with each waypoint. Waypoints may include flight (with varying altitudes and speeds), attacks, take-off and landing. In the same way, you can assign waypoints to the player squadron, giving the player an idea of how action will unroll, but also, depending on what the first waypoint is, whether you'll start on the ground or already in-flight, at a preset speed and altitude.
The 000:00:00 denotes what state the squadron will be in as the mission starts - as if you started a stopwatch at the mission start. So, if you go to the second (the one after the starting) waypoint, depending on the speed you've set for the squadron, you'll see the timer has changed to, say, 00:02:30. That means that two minutes and thirty seconds after mission start this squadron should reach the waypoint and proceed onwards.
I am by no means an expert mission maker - I've only started fiddling with it. Still, I hope this helps.