You can check in anytime. This last trip we checked in at 3am. It would be a good idea to call ahead and advise them you are running late. We were able to ask for an easier slot to get into so we could pull in, slide out, and go to bed. It worked well and hopefully we were able to keep noise to absolute minimum for our neighbors.
We did have to return in the AM to have our cards activated for charging because they had to manually process our CC at check in because the system was down.
I am assuming you mean a late check in. You may check in early, but it all depends if your site is ready. If it is not, you can still check in you just won't be able to occupy it. Check in time is officially 1PM.