It should work.
What version of Aeroscout Tag and Server Engine are you using?
When adding the aps in the aeroscout system manager, make sure that the ip you put in is the ip of the controller. You also have to enter the mac address of the ap ( you can find that in the controller gui, reports->ap inventory ).
Once the ap is added you can right click it and ping ( which should be successful ), and push the lbs config and get status.
Put in the ip of the aeroscout system manager in the wireless controller. ( also make sure that the aeroscout services are started on the system manager machine )
Make sure you set the channel selection in the aeroscout tag manager to be the channel the ap is set to. If you are testing, choose a channel on your ap, you need to be broadcasting at least 1 wlan service for the radio to switch on. Set to b/g for this model of tag.
Make sure that transmission is set to WDS.
Push the general and transmission setting changes to the tags.
I can send some screenshots to you directly via email.