Here's how the box pool works. In any game played, there are always 2 scores. The home team score, and the away team score. What's important for this pool is the last digit of each team's score, which can be anywhere between 0 and 9. As a result, there are 100 combinations of one team's last digit matching the other team's last digit (10 x 10). This makes it easy to create a grid with the away team's digit lined up top to bottom, and the home team's digit lined up from left to right.
To determine the matching box, you find the match of the 2 digits and find the matching coordinate.
There are 4 possible scenarios. The result of the the score at the end of the first quarter, at the end of the first half, at the end of the third quarter, and at the end of the game. Keep in mind that if there's overtime, the end of game matching box is determined by the final score, not the score at the end of the 4th quarter. Of course, the league commissioner can decide to change that if he/she desires.
The numbers assigned for each team is only determined after the box is full, or when the game begins, whichever comes first. The numbers are randomly generated by the web site. Once the game begins, no more picks can be made. When selecting boxes, nobody knows what numbers they will have. The numbers on top and on the left would appear as a question mark. If the boxes are not full, the pool commissioner can decide what to do if an unchosen box matches.
If the game is the SuperBowl, the AFC team will be the away team, and the NFC team will be the home team. This makes absolutely no difference, since all that matters is assigning numbers to each team.