Issues with automatic update on a rooted Epic 4g touch
My answer(s): (these are limited to my experiences)

No, you most likely will not be able to apply a standard update to a rooted phone. 

As far as turning off the update, this is most likely specific to the phone, and if it's being pushed by your carrier, my guess is you can't just turn it off. I would choose (now that you're rooted) to just flash a new ROM. If you like your stock stuff, you can probably find a ROM that is the same thing you're using now, with the 2.3.6 update. 

This ROM may be what you're looking for in the case I described. It doesn't require you to do a wipe either, basically the update for your phone!