In a standar install of ZC, if there ARE comments from a customer in an order, these are shown on the order confirmation e-mail in a "bright pink" box (div).
This is governed by the following declaration in the email styles data:-
Code:
.comments {background-color:#FF6699; border:1px #9a9a9a; width:542px; padding:2px; font-size:10px; }
You can put in a header quite easily, by "hard-coding" it into the appropriate place in the email's html...
Just open:
/email/email_template_checkout.html
... and insert proper html-formatted code into the comments div.