When setting up Orbot / Android version, to utilize it's beta VPN. It takes me to a screen with my Apps and more, each check box is not checked. Is this telling me to check any App that I want it to go thru Orbot VPN, and if so, should I check all boxes or just items that use the web?
I'd suggest using it for apps you want to use behind Tor, there are problems with picking random apps and sending them over Tor because many apps are very insecure and will, for example, send data in plaintext exposing them to risks from any potentially malicious exit nodes.
The best option is to pick privacy preserving apps, or apps that are designed to work with Tor, and use the VPN mode with them to help enforce Tor use.
But some apps seem to do things like use the WebView browser, which means that even if you pick the app itself to behind the VPN, using WebView seems to result in the connections originating from another app which may not use the VPN, resulting in leaks.
In cases like that, you could put everything behind VPN mode to better enforce Tor usage but it's not the best solution to the problem because two apps, which you are using for two different identities, might use the same circuit and accidentally link the two identities together. Further, some apps might take issue with connections from Tor and it could result in your account being locked or closed.
So, which to choose very much depends on your situation.
If you have apps that are designed to work with Tor/Orbot like Orfox or ChatSecure, then you should use the VPN with them only.
If you have apps that aren't then you might be best to VPN everything but that comes with the potential issues I've summarized above.