Do you have a thesis advisor yet? Your institution will probably have very rigid style guidelines for layout and formatting. Your advisor can guide you through that.
By using Indesign you are probably incorporating a whole other layer of unnecessary work, and frustration, for yourself. You’re going to spend what, 500 hours, writing your thesis, and maybe 10 hours laying it out? Don’t use a screwdriver to hammer nails into a board. Use the right tool for the right job. You’re going to be doing a lot of writing and editing, so use a word processor, like Word.
In Word, create custom styles for everything that match your university guidelines, and name them so they are distinct from Word’s default styles… Thesis Header, Thesis Footer, Thesis Page Number, Thesis Footnotes, Thesis End Notes, Thesis Index, etc.