How to deal with multiple affiliations as an author?
I'm professor at a university, which pays my bills, and I'm also affiliated with another institution, without any money involved. I do as in 2: I put always first my university affiliation and second the other affiliation for papers in collaboration.

It should be noted that in the recent past I had to fight with a journal because the copy editor arbitrarily changed the order of affiliations just to compact the list of affiliations.