Your question is unclear, but when I got my FBV MKii and connected it to my HD Pro, I spent the better part of two days trying to get the damn thing to calbrate using the methods described in the manual, but even more so, I could not get the wah to work with the foot pedal.
I found out, I was not pushing hard enough.
If you have the hd500, I am not sure if it is the same, but try pressing a little harder. It usually helps to stand and do it until you get the hang of it.
The FX Loop is for adding something into the chain outside of the Pod.