Dissertation Footnotes

I need the numerical footnote reference to be a size 12 font in the body of the text and a size 10 font in the footnote at the bottom of the page.  Right now, I insert the footnote at the end of the sentence and have to change each individual one to size 12.  I am about to combine all of my individual chapters with over 1,000 footnotes.  When I cut and paste it, I am concerned that I will need to go back and individually change every one of the numbers in the body back to size 12.  

Since I will continue to produce scholarly work, I would like to know how to do set this up where these will display correctly.  I am working in CMS/Turabian for the formatting of the dissertation.