Multi-WAN/LAN is difficult to traffic shape since you need a queue for every combination of interfaces you plan to shape.
Example
If you have 1 WAN and 1 LAN, to shape VOIP, you need one rule/queue
If you have 2 WAN and 1 LAN, you need 2 rule/queue
If you have 2 WAN and 2 LAN, you need 4 rule/queue
If you're just concerned about VoIP getting through correctly, you could try just enabling FairQ on every interface, set your interface bandwidth, and let us know if it helped.