I was not able to figure out the waypoint system either. The first level with 1 enemy was easy, in the second one I bought 3 ships. 2 of them went off alone without following waypoints and were obliterated. Then the 5 enemies killed me.
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Sorry about that! If you shift click you can select multiple enemies to follow a waypoint. You can also just click on an enemy and then click on the first waypoint in a path to have it assigned to that. I recommend giving the other two friendly ships waypoints and then right clicking the third to control and do a flank or other method to try to catch the enemies off guard. Thanks for playing our game, we will be getting to yours as soon as our schedule allows!