Hi Andy,
The IsToBeEmailed and IsToBePrinted fields are synced with the same fields in QuickBooks. Basically, if you check them you are flagging them in Method to be emailed/printed in Quickbooks later.
The actions for the Email notification when saving? checkbox is actually placed in the Save button. When you click Save a Conditional Statement action performs an "if" statement (ie. if the box is checked, send an email). This is common for these types of objects. Hope this helps to clarify!
Jason