[Drunken Mixer]

open the plug and click on "auto"
You should see a very long list of automatable paramaters. Select the paramater you want (wah) by clicking ADD. make sure you have automation enabled for plugins in your "automation enable" window. set the track to "auto-write." Unless youre using a control surface you'll have to use youre mouse to do the wah moves (Control surfaces rock!). press play and turn the little knob from side to side. You should be set. Or you can change your track view from "Waveform" to "Amplitube-wah" and draw the change in. Once you have enabled a plug's parameter for automation it becomes available in your track view list. I usually assign the wah effect to a physical fader and do it live in real time, then go back and clean and tighten it up in track view mode.
This is the basic set up for automation of any plugin, so Im assuming you haven't tried this on ANY plugin. If you have but you're saying it just doesn't work on amplitube, I've no idea what the problem is.
hope this was helpful. Let me know how it works out.
DM