Typically, you give your ships an order to follow the waypoint (ship dialog -> "Initial orders" -> "Waypoints"; note that FRED will hide the "Waypoints" goal unless there is an actual waypoint in the mission).
The best/most robust way to do this is to create a waypoint for each ship in the convoy, tell each ship to go to its own waypoint "Waypoints" or "Waypoints Once", doesn't matter) and set each ship's departure cue to check for when it's within a certain distance of its waypoint.
If you use a single waypoint for an entire convoy, the ships' paths will converge on that point and they'll start bumping into each other. Worse, they may never actually reach the waypoint, if two ships are colliding with each other trying to occupy the same space. This is another good reason to use a departure cue that checks for a distance, rather than a "Warp" order with lower priority than a "Waypoints once" order (which is the simple way to do it).
Note that ships in a wing will get into a formation automatically, and will all depart at once (you can only set a departure cue for the wing, not for individual ships that are in a wing).
Good luck! Glad to see more people making missions