It sounds like your remote users are using an ISP to VPN into your office, if this is the case then your issue is probably with their connection to the internet. Since the Internet is public you will have no QoS across it. I'm assuming you are using G.711 for all your phone calls, you could look into buying a couple of G.729 voice resources and trying G.729 to the 2 remote stations. G.729 uses a lot less bandwidth than G.711 so it might help, however G.729 compresses the call more so the remote agents will sound like they are on a cell phone.
As far as your registration issue goes I'm assuming you are referring to the Polycom phones are registering to the CIC server with a SIP connection address of "SIP:<Station Extension>@<CIC Server>:5060 in Interaction Administrator. Do you use a SIP proxy between your Polycom phones and the CIC server? Also, what version of CIC and service update are you running?