For the Wah Wah in Cubase 6.5 VST Amp Rack ...
1.) Assign a Quick Control for your foot controller (Chapter 26 Track Quick Controls - Connecting quick controls with remote controllers).
2.) Activate Quick Controls in your track's inspector area. Enable QC Learn Mode. Rock the Wah Wah with your mouse. Your pedal should now be operating the Wah.
3.) To record and playback the Wah movement, show your track's automation and select either WahWahPostPedal or WahWahPrePedal (you will need to select "More..." and browse through the folders Ins., 1-VST Amp Rack, Fx, Wah Wah, WahWahPost(or Pre)Pedal). You should see your pedal changing the automation value. Enable Write/Read and the Wah will be recorded as automation. Leave Read enabled for playback.
Same idea for the Wah Wah effect plugin.
Let me know how it goes.