I searched through the list for posts on how to use the emailing function for invoices, and found lots of discussion and changes in the development, but not any one piece of documentation in the web help of how to set this up and use it. I may be looking in the wrong place. Is there an article in the web help that explains it start to finish? I see in the contact manager, check boxes, and also saw discussion about using the primary contact field in an older post.  
 
Is there any flag or setting to direct the invoice to print to printer or email automatically when printing a batch of invoices for various customers with different preferences?

The print dialog box has options for Print, Preview, Email or File.  You have to choose email.  You can't print a batch of invoices and have the system automatically email some and print others.

When you DO choose to email it controls who gets which sort of document.