I have opened the template fro Bib. and footnote, changed the Journal from italics and the Title to Italics, saved but when I cite it still shows up as the original.
On reopening both templates the changes I made are still visible.
Are you using the correct output file? When changes are made to an output style file (e.g., APA 6th), the changes will be saved to a file copy (e.g., APA 6th Copy) upon exiting. So both EndNote and MS Word should be adjusted to now use the copy of the style.