In general, I’m unclear about what things, specifically, Reputations and Affiliations give their bonus dice to.
Circles whenever the person being looked for could be found better by drawing on appropriate Reputation or Affiliation.
So Rep and Aff only affect circles? I couldn’t gain extra dice on a resources test if I was part of the seller’s organization or had a mighty and intimidating reputation? No extra dice during social skill tests?
The only effect they grant is a bonus to circles checks. That said, the GM can grant advantage dice if they seem appropriate. If it seems like your reputation ought to help you, it could be handled that way. But that’s just an example of the advantage dice rules, not a rule about reputations and affiliations.
If you want an easier Resources or social skill test as a result of a rep or affiliation, you can make a linked Circles test that can leverage them.
Reputations and Affiliations already factored into your starting Resources attribute, so it’s already giving you dice.