When using Outlook Mail with Google Apps Sync for Microsoft Outlook®...
Use your new Archived folder.
Place messages here that you want to remove from your Inbox but keep around for reference. (You have 30 gigabytes of storage in the cloud for your personal Google Apps account so you won't run out of space!) The Archived folder also contains messages you archive using the Gmail interface, that aren't already in another folder.
Set a local Mailbox Size limit
This is necessary only if you want to store more than 1GB of mail in your local Outlook mailbox. Regardless of your local mailbox size, all your mail is available from your Gmail account in the cloud.
Make Google Apps your default account (over any POP or IMAP account)
You can add other mail accounts to your Google Apps profile, say, for personal or family-related mail, just as you can with Microsoft® Exchange. Mail sent to a POP3 account appears in your main Inbox along with your Google Apps mail, while mail sent to an IMAP account goes into a separate Inbox for that account. Just be sure that your Google Apps account is the default account in your profile (otherwise calendar invitations sent to your Google Apps account might not end up on your calendar). Do this in Outlook's Tools > Account Settings dialogue, on the E-mail tab.
Note that neither your POP nor IMAP mail is synchronized with your Google Apps account in the cloud. Nor will calendar invitations sent to your POP or IMAP account appear on your calendar.
Compose HTML mail, not Rich Text
By default, Google Apps Sync sets your preference for composing mail in HTML format, rather than Rich Text. Don't change it back to Rich Text or messages you send won't be readable.
Find your Sync Issues folder
Google Apps Sync creates a special Sync Issues folder that tracks synchronization performance. Most of the time you can ignore this folder. But on occasion, your administrator might ask to see its messages to help troubleshoot a problem. The Sync Issues folder is in your Folder List. To see it, go to Outlook Mail and choose to Go > Folder List.