"Who do we pay?"
Correct. "Who do we pay?" or more correctly, "Whom do we pay?"
Think about who is doing the paying - "We", therefore "Wir" is the subject. The question asks for the name of the person that receives the payment. In other words, who receives the action of the verb. The person/thing that receives the action of a verb - receives the pay - is the Direct Object, and thus "wer" takes on the Accusative case "wen" In English "who" becomes "whom"
It's a little awkward because the subject comes after the verb (something we don't do too often in English) which makes us immediately think the first thing is the subject, and the latter the accusative.
What I do is take my time to fully translate a sentence best I can. Enough to understand the gist of what is going on. Then I work out who is doing the verb, and who is receiving the verb.
It sounds silly easy, but when word order gets mangled you realize this is helpful. After a day or two you get faster and faster and the whole process becomes rather trivial