EndNote has two Chicago 16th output style files: Author-Date, and Footnote. Which output style file are you using? Neither Endnote style file includes a bibliography or footnote template for the “Manuscript” reference type so one needs to be constructed in order to display the reference information.
I would create a template for manuscript if you don’t use it for anything else. you might start with a template from one of the other reference types and edit it to retain the fields and add additional fields you use, and reorder them as necessary.