The reason to separate is that, according to Turabian 8, the footnote form should include the subtitle, but the short form should not. The regular form is used the first time a resource is reference, and the short form is used subsequently.
Actually, I found a great way of doing this. I’m using the “Title” to store the title with subtitle, and I’m using “Short Title” to store the title without subtitle. I’m using “Short Title” instead of “Title” in the footnote short form. The interesting thing is that if “Short Title” is blank then Endnote automatically uses “Title” instead.