i know that rory says no to logans proposal but do they still end up together?

Considering that when they filmed it, that ending was supposed to be a season finale, and not the actual ending of the show, I'd say it's up to interpretation. It was an open ending, so I guess it's whatever u interpret it to be. I, personally, think they did end up together, somehow, sometime... =D

No, they don't.

no they wold still end up together

They better do! ;)
I made my own happy ending. Open endings are not allways so good but now I just imagine she went back to him and zei yes :) ;)