Drop the new cork and screw set up screw first into the bottom of the head joint. If the cork is the correct diameter you should be able to see it partially through the embouchure hole.

Flute head joints have a tapered diameter that is smaller at the top. This will not work if the cork is put into the top of the head joint.

Use the flute tuning rod to push the cork into the head joint until the tuning line at the bottom of the rod is in the middle of the embouchure hole.

If the cork is difficult to push down, paraffin wax can be rubbed onto the cork to help lubricate it.