WAAS Flow Monitoring is very specific and these flows can be processed only by NetQoS and you will need NetQoS SuperAgent for this. The NetQoS SuperAgent processes the flows received from WAAS FlowAgent (which again was developed by NetQoS) sitting on the WAE. More details in the below link:
http://www.cisco.com/en/US/docs/nsite/enterprise/wan/wan_optimization/chap04.html#wp1053045
There is some solutions that does that using API; because Cisco let you do that. SolarWinds should do something like that to a future release.
