Clicking the Apple Mail button activates the Apple Mail window. You can select specific mailboxes, to transfer all of the messages contained within those mailboxes, or transfer all messages to your iPod.
You can restrict which messages are available for transferring. You can have only unread messages, only flagged messages, and you can limit the messages to only those received within a given time period. Each of these options restrict which messages will be transferred to your iPod.
Additionally, you can have Mail check for new e-mail before transferring messages to your iPod by selecting the Check for New Mail option. The first time you load the Mail window, and on every Sync operation, iPDA will tell Mail to check for new messages prior to transferring them to your iPod.
With Leopard (OS X 10.5) Mail allows you to create Notes and iPDA allows you to sync those notes to your iPod. You should choose to not store your Notes in your Inbox so that iPDA can process them as notes (otherwise the notes will appear as messages in the Inbox folder on your iPod). iPDA supports Notes on your Mac and on IMAP servers, with the IMAP Notes appearing in separate folders on your iPod.
With Leopard (OS X 10.5) Mail allows you to create To Do's and iPDA allows you to sync those To Do's to your iPod. This is done via iCal syncing since the To Do's are stored with iCal and Mail simply manipulates the associated iCal calendar. You can set the calendar for each To Do in Mail so to sync them to your iPod, ensure that those calendars are selected for iCal syncing. Further, you can create To Do's for an IMAP account and iCal will add a calendar for each IMAP account. Make sure you include those new calendars for iCal syncing. You may also want to rename the calendars in iCal since it uses "calendar" as the default calendar name.