If you're speaking of the BibTex sync file Bookends generates, it's unsorted (the order is undefined, but is probably in the order the entries were made). If you want it sorted for some reason, that's a setting in the BibTeX format. If you want some special sort (e.g. by reference type) you'll have to do that with the exported file in another app or perhaps with a script.
Jon
Sonny Software
P.S. You can always generate a Subject Bibliography sorted by reference type if that is something you need.