Did you actually
open the template or create a new document from it? If you opened it then File > Save should save it in the same format. Adding a bookmark shouldn't affect this.
I would also suggest replacing the bookmarks (which are all to easy to delete) with content controls. You may find
Insert Content Control Add-In useful in that task. It is then easy enough to write the values from the userform to the content controls - see
Create a userform.