You can check in online 10 days prior to your visit. They will prep all your key cards, etc., ahead of time. You can always put in brief/minor requests with your reservation, but generally, I've never found online check in to be any faster than the "old fashioned way." There are two separate lines, yes.
It is 60 days now. However, I think that is for when the FP+ roll out happens. I don't think there is any benefit to online check in so far in advance without that in place. We have always had a quicker registration when doing online check in, however, in the last five visits to Disney, our room has never been ready on arrival (which had always been in the afternoon) so it hasn't helped with that.
You will be asked to give a time of arrival and the CM will attempt to find you a room already available. It may not suit your requests and then they will need to look for a room that suits your requests and re-print your KTTW cards.
So if you have requests, there is really no advantage to it, until as the PP stated, the FP+ system rolls out.