The first thing you need to do, is to list all the functions you need in your design, like PWM, UARTs including control signals,CAN, analogue IO, timer/counters, USB, Ethernet.
Then you need to look through the pin/function list and see if this is possible to combine. Many times you will need to make a changes to solve the puzzle completely.
Sometimes there is not enough pins for the funtions you need, and then you'll need to redesign your needs, or change to a bigger processor/larger footprint, with the pins available. Most processor families have several variants of the same silicon, with more or less RAM/Flash/IO available.
This is also why we can't tell you which pins to select, since we only know a small part of your design.