I think the Flood units will just either be:
A) Not a playable side by you.
B) A side like the Aliens in Earth 2160.
http://www.earth2160.com/index.php
A brief description of the Aliens...(by yours truly)
They start off with 4 units, 3 basic "infantry" units, and 1 flying "vehicle" unit. They collect resources to fill up a bar, which when completed, makes them gain 2 (or more, depending on the level) options. One option makes them clone themselves, but the other makes them turn into a more advanced form. And of course, the unit types branch off, for instance, I'll use the infantry guys as an example.
When their bar is filled, they can turn into one of 2 things. A high form of infantry, or a base defending structure. That base defending structure can upgrade one more time, then that branch is done, it can't clone anymore or evolve. But if you do the infantry, you go through a completely different branch, eventually turning into artillery like units, or a very sophisticated tank.
Ok, no more typing for me.