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Microsoft Activesync will allow syncing of email from more than one folder besides just inbox. To allow syncing to more than one folder besides just inbox, open up activesync on your desktop and click on Options -> Inbox -> Properties. You will see all of you email folders there if you have more than one.
As far as Notes and Contacts, Activesync does not support syncing to subfolders for contacts. If this is something that is important to you, you may want to look at Intellisync as it supports syncing to subfolders.