Wrists first, leaving her helpless. With the condemned completely naked, position her wrists at about elbow width from her body to either side. Drive the nails between the carpal bones of the wrist, which are in the heel of the hand. Take your time, don't hurry the process. She can kick and writhe all she wants, but it will serve no purpose other than to entertain the onlookers and demonstrate that she is receiving full and just punishment for her crime.
Then, depending on the type of cross, either raise the cross or lift the patibulum into place on top of the stipes, allowing her to hang freely with all of her body weight on the nails in her wrists. Leave her to writhe and scream in agony with her feet free until she exhausts herself. Install a sedile or conu on the cross while you wait. Make her beg you to nail her feet.
Then when she's compliant, place the sole of one of her feet flat against the upright post with her heel almost touching her bare butt. Probing with your finger, follow the space between the second and third toe up along the top of her foot until you feel the depression end in the bones of the arch of her foot. Make sure she is watching as you place the point of a nail there; tell her that if she struggles, you'll leave her to hang longer.
With the hammer ready, make her ask you to nail her foot. When she does, pin her foot to the cross with the first blow of the hammer, then take your time driving the nail down the rest of the way. Pull her other foot up beside the first and repeat the process.