Apply rusty metal primer first, or even POR-15 or something similar to convert the rust to an inert form. Then come back with a couple of coats of exterior rated paint designed for roof exposure.
If you intend to use metal roofing paint, apply the primer that product recommends, as conventional paint primers may not be the best choice.
NOTE: Aluma-Kote only specifies a projected life of ONE year, so if you choose that route know that you're going to need to come back and hit it again, and again, and again. There are other products that have projected lifespans of seven and even ten years when applied properly and I bet that, while more expensive than Aluma-Kote, they aren't TEN times more expensive. In terms of performance per dollar and time required of you, you might do better to spend a bit more in exchange for a lot less effort and a more satisfactory result.
Good luck with it.