We use a different Apple ID for every site as well, so you can expect...
For every site, you'll have a different VPP. For every instance of a VPP you'll have an app. So in some cases you may have the same app listed several times in JSS - Mobile Device App Catalog, once for each site.
In the JSS - Mobile Device App Catalog, you either chose to prompt the user to install or to add the app in self service. Both ways will require the end user to authenticate the install with their apple id and password. So make sure you have someone you trust with this information authenticating the apps.
Depending on the number of iPads you're working with I find using self service or prompting the user to install apps very painful. It works, but it's time consuming unless you have a lot of help authenticating.
We recently made the decision to use Apple Configurator to install the apps if we're using a VPP with more than 10 codes. Because you can install the apps without touching each device to authenticate. If we have less than 10 codes on a VPP or the iPads are in a one to one environment in the hands of someone you trust with your Apple ID then we use JSS - Mobile Device App Catalog.
Hope this makes some since. Each practice works better for some than others. And in our case we're still trying to find the BEST practice, however for now the above is working for us.
Chuck
