There are several ways to accomplish this.
I would create the original document combined. Just before submission, you can make a copy (keep original for revisions), unlink fields (from endnote ribbon, “convert to plain text”) and separate them. - This way the figure legends will have the correct numbers for their citations even when in the separated document.
If outside (or even in the same document but at the end) How do you want them numbered? – If order of appearance and you want them numbered where the figure would appear, then insert a citation where the figure is cited, and right click, edit citation, and choose “show only in bibliography” which will make them invisible.
If they are alpha – just add them at the end and “show only in bibliography” (invisible) and you wouldn’t have to have the figures in the same document, BUT you will manually have to number the figures in the stand alone figure legends documents anyway.
Be sure your figures are outside text boxes, or you will find they get numbered 1, 2 3 if in order of appearance in the combined document, no matter where they are in the order of the other text. They should be in frames. http://www.extendoffice.com/documents/word/733-word-insert-frame.html#a2 for a way to do this in recent versions of Word.