One thing I’ve learned is that jazz band directors have different opinions regarding the best seating arrangement. Here’s my opinion!
I would recommend that you move the flute seat around the band to place the player(s) where they can best hear the other parts that they need to listen to in order to blend, balance, and tune. If the part is an “optional C” part and is duplicated in the Alto 1, then I would seat the player(s) next to the lead alto. If the part is a double requirement of another part, say Alto 2, then I would place the player(s) next to the Alto 2. Therefore, during any rehearsal and/or performance, they may be required to move to another place in the set-up. That’s okay. Put them where it makes the most sense to be based on the arrangement you are doing. I would definitely recommend moving them out of the trombone section.