Configuring QoS on your Catalyst 6500s in your Core/Distribution layers IAW Cisco's best practices means NetMRI QoS Module will not be able to monitor QoS for dropped packets in your Core/Distribution layers.
Here's the workaround: Configure the same policies you have on your access layer or simply a default policy on your Core/Distribution 6500s much like AutoQoS does on your Access Layer 4500s:
and on your interfaces (including Port-Channels)
service-policy input autoqos-voip-policy
I've only tested this on Sup720s running 12.2(33)SXH Advanced IP Services so on anything else YMMV.