Todd,
When you're creating your toolpath in PartsWizard or PartWorks, any cutting depth that's less than the stepdown value in the tool database for the bit you're using is fine, but the easiest thing is to just pick a very small cutting depth... something like 0.01.
The cutting depth values for your profile toolpath are ignored when it's converted by the virtual tool, but you just don't want to create a toolpath that cuts in multiple passes, because it will keep cutting the path over and over again.
Hope this makes sense,
Bill