It would be a good idea to have the squares at the wedding and make the quilt later. Give it to them either on Christmas or on their first anniversary. This way you can have extras available in case someone messes up a square. The pens are quite expensive and people tend to change their mind after they write something. The freezer paper stabilized the fabric, it tends to move and stretch when you write on it. Have a couple of baskets one for the blank squares and one for the finished squares. It will look nice and catch everyones eye.
Sue