Well, you do have to upload after changing the speed, since that setting controls how your program is compiled. The new speed takes effect when Teensy3 reboots after the upload.
But there's no other changes needed, like physically changing the crystal (as you would do on an official Arduino board) or editing anything else. All the timing stuff, like delay(), millis(), IntervalTimer, all automatically adjusts to the new CPU speed.
Of course, your program will run slower. If your code depends upon the CPU speed, you'll need to make whatever adjustments are needed in your own software.