I would keep in mind the following things...
1. Interception - You have to ensure you intercept the traffic outside the tunnels, otherwise you won't get any compression. Hardware based switches like the Cat6K cannot use WCCP on tunnel interfaces. Software based routers can do interception on tunnel interfaces, but don't scale as much as the hardware assisted platforms.
2. Packet size - if you are getting excessive fragmentation, try lowering the Optimized MSS value on the WAEs to under what you need for headers. WAAS default is 1432.
Other then that, what you have is a pretty normal installation situation.
Thanks,
Dan