What you could do is keep the main title in the Title field but 1) add a custom field (e.g., “Subtitle”) to the Book reference type to hold the book’s subtitle and 2) in insert the custom field in the Book output style’s bibliography template. This allows the footnote to show just the title but the bibliography entry will show both the book’s title and subtitle.
Refer to the Endnote Style Editing guide which is available here http://endnote.com/kb/131728 and refer to the following sections for adding a custom field to a reference type, and adding that field to the bibliography template:
1.4.2 Adding, Deleting, and Renaming Fields
3.3.4 Adding and Removing Fields in a Template