I’m guessing there are many ways to handle this; this is just the one I feel comfortable with :). I like it because it shows me the things I still need to do in the resulting document. So when I read a draft of my masters degree, I will know what needs to be fixed.

This will create two places where to see the “fixme”: 1. in the footnote on the page where the “fixme” was written and 2. at the point where \listoffixmes is executed. Both these reminders are very useful when proofreading a document. You’ll have a “bird’s eye view” with the index and you’ll have specific context with the foot note :)