To customize an Agreement to an individual client, click Customize before you issue the Agreement.  

You'll notice a Customize... button when issuing an Agreement for when adding a new client:

You'll also notice the Customize... button when issuing an Agreement to an existing client:

When clicked, you'll be presented with the template you have selected, and you can customize from there. 

Customization cannot be done after the Agreement has been issued, so make sure to do these changes before sending. Otherwise, you'll need to delete the issued Agreement and reissue the modified version.