I've been thinking how the flood would operate and I came up with this:
The flood race should be as the flood were in the Halos. All they start with are little, fragile infection forms. They can be made as easily as they are destroyed.
This brought me to the Flood's first ship. A mobile incubator made of the yellow-green Flood-flesh

. It is propelled through space by ejecting certain gases because the heat of an engine might disturb the incubation process. Inside the bulbous mass that is this transport are sacs of Flood spores and infection forms. The spores are released into the planet's atmosphere which will slowly change into an environment that nothing could ever live in without a breathing device. The infection forms enter ships and assimilate the crews.(colony/siege)
Ships so fragile as that^ could never expect to capture ships without escorts to occupy the soon-to-be hosts. So I recalled everything I remembered about the Flood. I remembered that the Flood had Pure-Forms, Forms of the flood that were capable of being created without hosts. If the Flood could produce vessels that could travel through space, they had the pure-forms. As I remember, there were three, a stalker, a spike shooter(*shivers*), and my least favorite, the tank. They would be the scout/light frigate, LRF, and the Heavy Cruiser which would literally be a meat-shield!
The Flood should be like the Rouge, they have ships of their own, but if they are to win, they can capture ships. Though they do have a colony "ship".