"In what currency do you pay" is very unnatural wording and would probably be better as "What currency do you pay with?"
I was taught to never dangle my prepositions, which means, to not end a sentence with a preposition.
But it's too nice. It's not a grammatical equivalent of the Polish sentence.
I would actually consider "W jakiej walucie płacisz?" to be a more general question than "How are you going to pay right now". No one in any shop, restaurant etc. would talk to you using "płacisz" unless they personally know you well enough, like when your friend is a bartender somewhere.