The call status window that appears when you place or receive a call will normally close when the call ends after about 10 seconds of inactivity. You can re-open the last call status window by selecting "Phone Amego -> Recent -> Call Status -> name of telephone device".
Any time the call status window is visible, you can hang up or cancel a call by pressing Command+Close in the upper left corner of the window. If you want to remove a call status window without cancelling a call in progress, press close. This will close the window (or optionally minimize it on to your Dock) without rejecting the call. Clicking the icon on your Dock will re-open the window. When the call ends, the window or Dock icon will disappear.
If you select Hang Up from the Phone Amego menu while more than one phone has an active call, any active calls will be cancelled. To cancel a single call when two phones are active, open the corresponding call status window first and select "Hang Up" from the action menu, or press Command+Close.