> I understand that you have to design the schematic and then get the PCB layout done, but in terms of figuring out which pins to connect, is it just a matter of figuring it out from the microcontroller manual?

yes. if you're using ST parts i suggest using their CubeMX tool, if only to figure out pin assignment. makes it way smoother.

i've seen multiple real projects with real engineers who should get this shit right screw up pin assignment.

also seen them just... not read the data sheet. i don't understand how they expected the board to work, but, it happened.