Alright, after toying around, I've figured out that your best bet for this sort of situation is to have the allies and enemies start off on the map duking it out. Watch the fight and try to get a feel for about how long it will take your allies to lose. Then, still on Wave 0, set the delay to about that point. That way, the player ships will gate in right about when the allies lose. Then, when they mop up the enemies, the next wave will come in. Setting the player ships to Wave 1 won't work, because waves are determined by the destruction of all enemy forces. If there's enemies left, no players will spawn in. Hang tight, I'll edit this post with an example encounter.
Here's an example of the above, in practice.