I would follow print for the sidebars and repeat them in appropriate places on the pages that repeat them in print. They are there for a reason and that is to tell the student what to do at that particular location in the print.
On the red words parts in the spelling pattern boxes, I agree--use italics. Section 5.8 covers this exact situation and specifies that italics is used for emphasized letters within words regardless of the way in which those letters might be emphasized in print.
Thanks for sending the print examples.