I'm assuming you have a mother on the tree and you want to add a father that is already listed somewhere else on the tree. You should:
1. Delete "Father of ..." from the parent pair if it is there. Just leave the mother. (Click on the "Father of...", select change or delete etc.)
2. Click back on the mother's entry and select add partner/ex.
3. Click on "Partner with person allready on tree."
4. Select the person from the drop down list.
5. Click on the appropriate Add as... button.
Should work but haven't tried it myself.