So... this topic is interesting as... Thus far the flood have been far more than a simple annoyance. Hell I could only stop them with the fully upgraded anchor stations. So they are already deadly, and can already colonize worlds etc. But they don't seem to be very intelligent... In that, they simply swarm, and destroy. Before the more impulsive people start yelling at me that the flood DO indeed swarm and destroy because that is their thing... There is more to this.
In the halo lore. The flood gain the intelligence of any individual they absorb. The flood are also a collective mind that can function to some degree on its own, but functions far better with a grave mind. The grave minds do not travel with the flood, they are constructed by the flood forms. For example. Halo one, remember the scene, inside of the infected "Truth and Reconciliation", you know the one I mean. Where captain keys is inside of that strange fleshy sac, and John punches into his skull and takes his implanted chip... That was the beginnings of a grave mind. The flood gather the more intelligent of the lifeforms they find, and feed that biomass into the sac until it grows into a grave mind. Once fully formed the grave mind is completely invulnerable to everything except starvation (IIRC)
So... The flood learn as they absorb, in halo 2 they learned how to fly space ships, by absorbing pilots. They learned how to fly high charity to earth, by absorbing pilots. The point being that they LEARN.
So feasibly, absorbing technicians and engineers aboard a frigate factory, would enable them to construct those frigates, in their infected form of course. So if they took a titan factory... I don't think they would construct a grave mind, I think they would instead use it to construct the biggest, meanest spore dispenser you've ever seen. (Flood Guardian + Spore Carrier + A whole bag of all the steroids)
As for making them use this knowledge. I think they should have two different flood types in the game. The "Pirate flood" which is the current flood, which functions independently of player actions, and does what it currently does.
The other should be a faction, allowing you to set an AI faction as them (while keeping them unplayable by the player) They would have a grave mind as a capital world, and would operate more like an intelligent AI, the bonus of having them as a faction is that you would be able to set their difficulty and the amount of them beginning in the galaxy, to tailor to your scenario.