How to use Chicago Manual of Style with superscript cite numbers and sequential endnotes instead of footnotes?

Almost  – but you are still using endnote’s  CWYW, but you are inserting them into the footnotes/endnotes and not citing in the text itself.  That is the difference between a footnote style and and and in text style. – EndNote still controls how they appear in the endnotes and how they appear in the bibliography.  They are separate templates in EndNote’s Chicago  output style.