There's no call waiting tone with IP phones on call manager.  If A phone calls another and it's busy the call will either go to voice mail or the caller will get a busy tone.  There's no way for call manager to check if a phone is on another call, still present the call and let the calling phone know the called phone is busy by playing a busy tone.  The best thing to do is to change the busy trigger to something other than one so the called phone will see the other call even when they're on the phone.  However the calling phone will have to wait for the call forward no answer (CFNA) to send them to voicemail.  This is like many cell phones, if you call a phone that's already on another call, the called phone will hear a a beep letting the called phone know there is another call coming in, but the calling phone will still ring as usual until eventually the call goes to voicemail.  The problem here is that either the call is delivered (the calling phone hears ring back) or the call is not delivered (doesn't ring the called phone) and the caller hears a busy tone.