Apple does not take a firm stand on whether or not the username should be entered in domain\username format or with only the username (omitting the domain), but in most environments domain\username is required. Typically, this depends on the default domain option for an Exchange environment (as well as whether or not the environment exists in a multidomain network), but in some situations, the full domain name may be needed even if the default doesn't use it. It's wise to test with an iPhone before developing instructions for users or support staff.
The iPhone prefers connections that encrypt all communication using SSL. If it cannot establish an SSL connection to the server (or in some environments to a Windows ISA Server), it is designed to attempt to connect without using SSL. Ideally, you should configure an environment that requires SSL.
If you are using SSL, you will also need to ensure that any certificates used to sign communications are installed on the iPhone. The iPhone ships with root certificates for a number of common certificate authorities. If you use certificates signed by these authorities or certificates that build an effective chain of trust, you will not likely need to install additional certificates on the iPhone. If you choose to use self-signed certificates or are relying on certificates signed by a certificate authority other than one available via the installed root certificates, you can use a configuration profile to install the certificates on each iPhone that will access your environment.
Once an iPhone is associated with an Exchange account, users will be prompted to enter a passcode that conforms to any policies established in Exchange. They will also have the option of choosing which types of data to sync -- Mail (Inbox), Calendar and/or Contacts. Once the iPhone has established a connection to Exchange, it should initiate a first sync (for performance issues, you may wish to have users establish their initial connection using Wi-Fi within your network). By default, the iPhone will sync only three days' worth of Mail items, though this can be changed using the Settings application on each iPhone.
Note: An iPhone can be associated with and sync to only one Exchange account.
iPhone ActiveSync feature limitations
Although Apple has implemented a number of Exchange functions on the iPhone, it has not included all the features found in Outlook or on Windows Mobile devices. As mentioned earlier, the iPhone will sync a user's Inbox, calendar items, and personal contacts using direct push and ActiveSync. It will not sync tasks created in Outlook, provide management of personal or public folders available in Outlook, support the opening of links to Microsoft SharePoint server sites, let users set out-of-office autoreplies, create meeting invitations using the Calendar application, or support flagging of messages (such as for later follow-up).
It is also worth noting that at this point, direct push notification and sync occur for new e-mails only if they are delivered to a user's in-box. If users create filtering rules in Outlook that filter incoming mail into other mailboxes, the iPhone will not receive push notification of their delivery (though opening the mailbox in the iPhone's Mail application will cause it to be synced manually) because only the in-box is monitored. As a result, users should either remove such rules or configure them to be run manually when they are at their computer.