We made some requests when making the initial reservation, but these aren't showing up when I tried to online check-in. Should these be in the "confirm or add special requests" section?
No, existing requests that are on your reservation will not display on the online check-in page. They're not changed or removed by the online check-in process, so no worries, they'll still be there.
The only options it gave me for requests during online check in was what floor I wanted to be on! Since the only request I had made was for an enclosed balcony (staying at WL and like the added privacy) I just selected "highest floor" hoping to reinforce my initial request.