The order of the Bibles in "Compare" is the same as the tabs but you can hide Bibles with Bible menu "Bible compare settings" but it is better.
Change the name of the Bible modules except the default modules (KJV, KJV+ and Strong, TSK)) by adding numbers before the file name.
for example.
001__first Bible.bbli
002__second Bible.bbli
It was easier with e-Sword Library Manager but that program needs to updated for the new modules.
http://www.biblesupp...0#commentsStart
So I ask someone with programing skills to update the program.