I have only ever done the online check in, and it seems to have worked okay, but I was wondering if there is an even better way to do it. Also, can you request to be in a specific room number?
I usually make our room requests when I make our reservations (by phone). You'll have to call if you want to request something other than what's offered at online check in.
Sure you can request a specific room. But the odds on getting it are remote. And then what? Better to request a specific range of rooms (ie: bldg 5, 2nd floor, facing the courtyard at POFQ).
You can do it while make your reservations online (to a degree) but it's better to do it on the phone, where you can be more specific/clear... But as @Minnie Mum mentions; don't get too specific.