Obviously start by rough aligned using the lines on the four jaw face. A bit of low cunning with a depth micrometer or the probe on a vernier / dial/ digital caliper on the outside of the jaws can help get it a bit better.
Put a suitably hefty bar with the end accurately perpendicular to the axis or similarly accurate and decently rigid L shape in the tool post to act as a setter reference. Something around 1" x 1" bar or 1" wide L will do. Run it up until it contacts the side of the square being centred. Lightly rotate the chuck bar and forth so the contact is true to the side. Note cross slide dial reading or zero dial. Retract setter, flip 180° and note dial reading. Re-set cross slide to halve the difference, remember backlash, and adjust four jaw to bring the square bar up to the setter. Flip 180° and check dial reading should be close. Repeat on the other sides. Go round again if need be. Quite possible to get a thou or less TIR.
Best to have a cross-slide stop when using a dial gauge so you can withdraw the cross-slide to get the gauge safely out of the way before rotating to the next side and go back to same position. One day you will forget. Even if its a fancy one with locking retract lever, mine would have been mega expensive at list price!
Make a note of the TPI or pitch of your jaw adjuster screws. Gives you a good idea of how much to turn them when adjusting. If you don't do a lot of four jaw work you loose the feel for how much a fraction of a turn shift things.
Clive.