Yes, you can put an author's note labelled "Warnings" at the top of your chapter, and list there any codes you think you may need for the story. We most definitely do NOT count those as author's notes for the word limit on those, and in fact, we're much happier having the warnings there for readers rather than to have readers upset by being surprised.
Most of the story codes are pretty straightforward, but if there are any you're not sure about, we're always happy to explain them, here or in email if you prefer. You can reach the moderating staff at this email: tos_team@adult-fanfiction.org