Going for the Upper Section Bonus is one of the main goals of the optimal strategy. To hit the sum of 63 needed for the Bonus, on average, you'd need to get three dice in each of the upper section boxes.
Typically, it's optimal to hold off on filling the Chance box, unless you have a sum greater than 20.
If you end up with a bad set of dice after the final roll, one strategy is to take a low score in a less important box like Ones or a difficult box such as Four of a Kind or Large Straight.
You can select a category even after your first roll; you don't have to wait until the last roll.
If you don't roll anything good on the first roll, it's often better to reroll all five dice instead of holding anything.