Do not stack them in a box as mold is a problem in the drying process. As soon as the flowers have dried, extract the seeds by rubbing two flower heads together. They should come out fairly easily. Sunflowers are also used as dried flowers and in craft projects. They can be cut just before the flowers die off and dried over a few weeks.
Miniature sunflowers make lovely fresh bouquets also.
For craft projects it is important to leave a sufficient amount of stalk. Peak harvest time is actually a little late if you want the whole crop. The birds and squirrels will begin their assault before the seeds are completely ripe. While we enjoy sharing this crop with wildlife, you can protect against this annual invasion by covering the entire flower with an old nylon stocking, a cheese cloth bag or any other covering that allows light and especially air to flow through. Do not use plastic bags as moisture buildup will rot the flower and heat buildup will scald it.