I think I understand now... hmmm... I am pretty sure you could do this with an app called "tasker," but that might be overkill. Maybe you could select different notification sounds in your e-mail and SMS apps. Make the e-mail sound something really quiet, but have something more audible for SMS pages. I have three different e-mail accounts I track -- each of those has a different incoming mail sound -- and my SMS, using Handcent, also has a different notification sound. That doesn't help with different times of the day, though...would just give you quiet or silent e-mail notifications.
Maybe someone else will have a suggestion.