I’m not sure I can speak too much to your first question about Tier. I’ve always handled payoff and rep as occurring simultaneously, but I can see that being something that occurs on a GM-byGM basis. When in doubt, ask the players too!
Glory Incarnate is great! One way you might introduce some sort of godly avatar is create an expert that manifest from time to time (maybe scaled up a bit to be tier+2 instead of tier+1 depending on how grounded your version of the Dusk is, or maybe you increase the scale/potency/quality of said Avatar in various ways so that the effect it has on the world reflects the deity’s power). The success of the avatar or effect could then be represented with a fortune roll, but thats just one way of doing it. In terms of RP, you could customize the avatar’s tags & flaws with stuff from the book or things pertaining to the cult (perhaps a keyword or two from the “God Features” in the Cult crew sheet? For example, a God of Slaughter’s Avatar could have Tags & Flaws like: Ferocious, Fearsome, Sinister, Wild). For another spin on it, maybe the God sends a flock of minions or a supernatural entity or effect that could be designed according to the magnitude table (p. 221 I think).
That being said, it also depends on how established magic is in your conception of the setting and how overt/not overt it is. To me, players taking Glory Incarnate has always spoke of things seriously ramping up in the real & spirit world, but theres no reason it couldnt be say, a creepy insidious manifestation that sneaks up on players as a consequence rather than something more overt (which is not to say it couldnt be both mind you).
I’d say ask lots of questions, then build on the answers with manifestations that reflect on what the players establish in the fiction. For example, you could ask the PCs: what do their characters fear most about this newly manifested Glory Incarnate? What they respect about it? How do the former two questions apply to the PCs contacts and enemies? What are other factions with hands/tendrils in the occult pies saying about these manifestations? Why do the PCs think the God has chosen now to manifest? Are they right? How do these manifestations relate to the Ghost Field? Do they relate to it? You can take what the players say and incorporate those answers in a way that the whole table can use them as great RP moments if thats the sort of thing your playgroup is interested in
Anyways, I hope that helps some! Sorry if anything was confusing or hard to understand, feel free to ask if theres anything that needs clarifying.