Make sure that your readers can distinguish the importance of your notes and warnings. Don't water down the severity of your message. I've seen some directions that had pretty serious warnings in footnotes.

Notes are for suggestions and ideas. Warnings should be clear. (We use red too to emphasize the text.) Make sure that the text is prominent and clear.

If you have a serious warning, put it first. You may consider using pictures, especially if your work is translated into other languages.