It might help if we knew the router make and model. However, I assume Sonicwall and I also assume the same in use at each remote site.
QoS may or may not solve the issue depending on the cause. It is not clear if the connections are symmetrical or asymmetrical and if the call issues are heard by the caller, callee or both. If all remote sites are the same size and if all have the same issue and if the VPNs are used to route all traffic or merely the voice and/or some other subset of data.
You may need to use BMW in conjunction with QoS to insure that there is enough bandwidth set aside for the phones.
I have attached an article that explains how to set QoS for Net2Phone use. This may help you, but of course, the ports are different. I am guessing that you want QoS for voice along all paths for both ingress and egress so the set-up for the main and the remote would be different due to the interfaces used. I am by no means a Sonicwall expert, so if you have a maintenance or support agreement with Dell on the products, I suggest you engage them.
My simple take on it is that you need both ingress and egress rules at all locations and at the main site I tend to think this would involve the LAN, WAN and VPN zones (all the interfaces are used for voice) and at the remote sites the LAN and VPN zones.
Once you have the proper tagging in place (EF), then you should be able to use Wireshark to confirm the results.
Not sure that I addressed the need, and as stated, I am no expert with Sonicwall, but hopefully the article will shed some light.
https://www.net2phoneoffice.com/PDFS/En ... rewall.pdf