Qos deployment not achieving desired results

Network setup – We are the hub to several remotes sites. Hub has 3 MB WAN connection. We host the central ERP system accessed by every remote site, as well as the central point for all email.
Testing involved one remote site with a 1024 WAN connection, all other remote sites have T1 WAN connection.
Using GRE over IPSec as well as Cisco WAAS throughout every site.
Problem – when email (no attachment size restriction), ftp, or sharepoint traffic traverse to WAN sites our ERP application (HTTP traffic) suffers timeouts.
Proposed solution – implement Qos to alleviate ERP timeouts and overall line degradation.
Set qos to mark ERP traffic as mission critical (DSCP af31) The WAAS is set to copy DSCP values.
Tried setting class to “priority bandwidth” – does not work since hub has 3MB connection and class will only be utilized when line is congested.
Set class to “percent” or “kbps” – “kbps” currently in place, dedicating 1533kbps to class marked af31
Matching packets now have a drop rate of 4 %, were as before we were not experiencing any drops.
End result is still that the ERP traffic gets degraded once the line is congested.
Desired result – Need dedicated response on line for ERP app regardless of amount of traffic that is on line.