Acrobat Pro gives you many type of ways to communicate and collaborate with others while you are working out the specifics of your layout. These can be very useful for you and your designer to get all the details just right.
What you should not expect is that those elements will actually print in your book. They are separate from the post script information of your file that will actually get printed. They should only be used on your end to communicate a change that will be made in the source document, which is likely Microsoft Word, or Adobe In-design or Illustrator. The final PDF supplied to BookBaby should be free of any annotations, comments, sticky notes, or elements pasted into your PDF in Acrobat.
If you are not sure if your PDF has them, like always, we suggest you order a proof copy first so that you can see how your printed book will turn out.