Your post is confusing. According to your setup, the second call to your home GV number is being routed through CC. Therefore, the incoming calls should be routed to SP3, not SP2!
You haven't indicated how the SPs are distributed between PH1 and PH2. Is it:
Phone 1: SP1, SP2
Phone 2: SP3, SP4
If you want callwaiting alert to "beep" (and/or show caller id) on incoming calls to SP3 (you GV incoming line), while using the Phone attached to Phone Port 1, then your incoming Call Route must reflect that. In other words, the setup should be:
Phone 1: SP1, SP3
Phone 2: SP2, SP4
Of course, the appropriate callwaiting boxes need to be enabled.