You do not mention platform or the number of devices, so I'll just give you some general items I have come across.
If you are on 5.0 or >, you can schedule your deployment of apps to a certain time frame period.
The ease at which your application will update will depend on the vendor and their code. Some are more graceful than others.
Due to the newer security features of the newer OS', you cannot get around the device notifying the user of a change in permissions or aka a silent install. That said, you have default settings that the app takes in the soft config. Even if your user changes this, the default settings will push out within 4 hours to your devices. The best you can do is to notify your users of the change, so you don't get emails/calls asking you about some pop up requesting https access or etc...
Good luck.
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I'm actually lost...
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