Yes, you can create custom Templates and save them. Then you can also save them as the “Default” template for that VST/Synth/Program as the Automap software allows you to see & edit the control of the VST’s.
afa the scrub feature, I have Cubase 7 and have never tried to program a scub. I’m pretty sure that there is a way even if it can’t learn it or program a work around
e.g. Setting up marker points and setting the xfader accordingly…
Also, I haven’t attempted to program anything for Cubase (yet) since I just got this but so far the transport controls and everything else work right out box…
There are a few videos and Info on their site…
I’ll also open up C7 and see if I can get the scrub programmed to the Pitch/Mod for ya 
Check out Automap HERE
Check out the ZeroHERE
