Give each Group the waypoints you want. Now click on "Synchronise" at the top of the mission editor screen (or hit ... F5 I think), left click and hold on one waypoint and drag & drop the blue line to another waypoint. These two WPs are now synched. When one group arrives at its WP, it will wait for the other group to arrive at its WP: then both groups will move on at the same time.
You can synch as may WPs with each other as you like. If you have 4 groups arriving I would synch everyone with everyone - looks a bit messy but makes sure you get what you want.
Hope that makes sense
If you head over to the Ed Depot - Tutorials - Getting Started you will find several good tutorials on waypoints.