I assume when you had the app tunnel configured it was shown within the 'resource assign' within policy editor?
If this is enabled it should be visible when a mac user logs on to the webtop. The only thing mine didn't do was to launch the remote desktop on the users machine. This had to be launched manually but I could then see the traffic passing over the tunnel when connecting to the correct RDP server.
I had it configured very simply, app tunnell to a specific IP/Hostname on 3389. This was associated within policy editor to the resource assign, then a full webtop. That was it..
Seems a bit odd if the app tunnel is not shown on the webtop.