It's not a QoS issue. If you had MPLS between the sites, then it is. Are you running CM or CME? If CM, the problem is you don't have enough bandwidth suitable to handle the amount of calls you are sending across the WAN and not have it be choppy. You need to configure locations/regions in CM to send G.729 across the WAN and use locations as a CAC mechanism while configuring AAR groups to send the calls out the PSTN if there is not enough bandwidth available. Test, test, test. If it is CME, under the dial-peer configure the maximum sessions going across the WAN while having another dial-peer with the same number with a higher preference match the same number (and use translation patterns accordingly if needed) to send the calls out the PSTN.