I don't think the actor's had much say in who ended up with who, either, but their preferences was pretty well known. Josh definitely wanted Pacey to end up with the girl and while Katie usually came out with the appropriate
PR response depending on which character Joey was currently dating, I think it was fairly obvious though that she slanted more towards Pacey and Joey. And after the finale aired and DC wrapped up she made it quite clear more than once that Joey ended up with the right guy. So there you go!