pin assignment

In one way or another, you have to do the pin assignment manually.

Some EDA tools have options to allow you to change the pin assignment directly in the tool, which makes it easier to change the pin assignment to simplify board design.

But in the end, before sending the PCB to production, you always need to

a) compile the design in Quartus and see if there are pin assignment errors

b) check you board against the .pin report file produced by Quartus

c) check your board against the pin assignment guidelines

That TimeQuest error is not a concern for pin assignment.