There is quite a lot of information on this forum site relating to getting your bees into the Flow super as well as in the FAQ section.
I waited until my bees had covered every frame and began building comb in the roof, it was also during a nectar flow in the middle of summer. In your circumstance, seeing that you are going into Fall I would reconsider having the Flow super on unless your winters are mild and there is some nectar around that the bees will collect and stor before winter sets in.
https://www.honeyflow.com/resources/faqs/why-arent-my-bees-filling-the-flow-frames/p/194