Add them to the secondary, you don;t ant to add them to wort. Add them to the finished beer. You can freeze fresh cherries which will cause the fruit membranes to rupture. If you are concerned about sanitztion blanch them in boiling water before freezing.
You may actually have to use a tertiary fermenter because when I have used cherries in the past it was very difficult to rack off the beer without picking up bits and pieces. Another option might be to use a puree.