Even if you do online check-in, you can still get a different room when you get there. We have changed rooms at the desk twice after doing online check-in. Once, at AKL, b/c the CM really wanted us to have a better view (her idea, not ours, lol!) and the other at AoA b/c our assigned room wasn't ready yet, so the CM gave us a choice of 3 others that were.
So it really can't hurt you, only help. And I've never seen then line be longer - usually shorter or maybe about the same. Though I don't think I've ever seen a significant line at any check-in, just one or two people waiting usually.
I think online check-in is 60 days out, but I'm not positive. It used to be 10, but I was thinking it changed with FP+. Your
MDE account should tell you how many days until you can check in though. And I've also made changes to a trip after doing online check-in, it doesn't matter. After I changed our dates, I went in and did the cjheck-in again just in case, though the CM on the phone told me it wasn't necessary.