What I ended up doing for the sub-folder sync was to modify my outlook rules so that they run on the client side only. This makes it so that they only work when outlook is open and exchange delivers all mail directly to my inbox. That way if I am away from my computer I make sure that I close Outlook, then when I am at my desk I open Outlook and as it syncs with Exchange it moves the mail from the inbox to the appropriate folders.
I know that this is not the best option available but that is what we can do for now. I would suspect that the next update to built in email app will have the ability to select which folders to push.
When I ask this question everybody told me to use Touchdown, I tried this app but did not really like the poor integration of contacts builtin contacts tools and it felt a little too cutesy for me.
Just my $.02!