This is exactly the reason why I wrote this software, as linked in the thread above:
http://pages.sbcglobal.net/kobe/ROMSorter.zipThere is currently no documentation, as I think there has been a grand total of one other person that has used this so far (to my knowledge). I can throw a little document together if people really want to use this, as some of the features might be confusing at first.
I remember there being another utility out there to perform this task (was it GoodTools-related?), but it was not customizable. Everything was hard-coded as to how the ROMs were chosen, so I ended up writing my own version. If someone does want to use this I'll be happy to answer any questions about how to run it. Some of the basics were explained in the thread linked a few posts back.