I think the launch checklists cover it somewhat well, the main thing you have to do is put the LV GUID switch to CMC, or else no kind of command from the CMC to the IU is coming through. Also, this only works on Apollo 10 and later as the CMC software didn't fully support it previously. For manual control you also have to do a V46E before commands are getting through to the IU.
Taking over control of the Saturn during powered flight only works if you get a IU guidance reference failure. Basically the IMU in the IU failing. You can get a guidance reference failure by using the PAMFD to randomly or at a scheduled time get this failure.