Call And ask for your preferred building NOW through reservations -- you need your confirmation number. There is nowhere to do that on Online checkin
You should ALWAYS use online checkin at POFQ, it literally means about a three minute wait if anyone is in front of you, and most usually just a walk right up to the checkin counter. I've done it a half dozen times over the past couple years.
It will make no difference as to upgrades assigned -- in fact, for people that are single, traveling without kids, it frequently results in upgrades because it allows the reservation folks to figure out who goes where, what rooms remain open and sure to be unbooked, and move people around. They almost always prioritize travellers without children first.
Note that is is VERY rare for a family travelling with kids to get an upgrade -- they assign the rooms way in advance based on number in party AND number of children in party. In general reservation terms, an "Upgrade" is frequently seen as an "inconvenience" to many actual resort guests.....you might get a river view at POFQ -- but it will come at the cost of being in a further building. Personally, I wouldn't consider that an "upgrade"...
You have a better chance of getting what you want by just calling reservations and asking for your request in advance.
As to which building you should stay in at POFQ -- if you have never stayed there before, you will quickly see it is a small resort -- you can ask for buildings 2,3,4,5 to be central (they also tend to be louder)....but note that there are only 4 other buildings outside there so at most you are one building removed from the Mint/pool. I wouldn't worry too much about it at POFQ.