Theses Requirements: Document Structure

The Bibliography/References need to appear before the Appendices.  A thesis is supposed to be able to stand without its Appendices, but it cannot stand without its References/Bibliography.  Because of this, the   If necessary, Appendices can be in supplemental files, whereas the References cannot and are not.

Check Step 1 (1.1-1.7) in the 3-Steps to Submission to be sure you haven't unintentionally changed something in your document. 

Publication manual formatting specifications apply when you are submitting to publishers / journals for review however, for the final copy, publisher and journal specifications are different.  Therefore, layout-related specifications such as margins, line-spacing, font characteristics for headings, etc. are a different matter and these vary from publisher to publisher and journal to journal.  For example, journal articles are usually single-spaced in the final publication and references are single-spaced with spacing between paragraphs. One can see that the layout in the final publication has changed simply by comparing the end result to the initial submission.  So your thesis is being published by the Library (and you,) and we are fine with the headings and spacing as these are set in the template.  However there are important features of APA, for example, that need to be adhered to, such as citing and referencing, when to use Arabic numbering within your text (rather than words), when to use italics for key terms, etc....