You don't want not-merged sts, you want either split or fully merged ones. Not merged ones would be a complete waste of diskspace.
Datfiles aren't needed, cmpro can import the data directly from the mame binary (Profiler->Create).
Secondly you should ask yourself if you don't want to use the latest MAME which is .180. (an update from .78 to .180 however is a huge step though....)
Generally speaking, the merge mode does not really matter, updating sets is always the same:
a) Either a full scan with all check/fix options enabled, look at the result listed in the scanner tree window and try to get the missing files (which then can be added via the rebuilder).
b) ...or you do a full rebuild from your old stuff to a new place once with the updated database, then a scan to see what's still missing...and then with the next udpate you do the a) thing
Actually, I think I do want a non-merged set, however I may not be thinking correctly, because I'm still very new to all of this. I believe (at least with the .78 set), there is only about a 25% storage space difference between split and non-merged complete set. I'm using a 128GB micro SD, and only using about 1/3 of the set on my machine, so space is not a problem. Also, if I went with fully merged, I would have to rename all the files to the one I want, and that would take waaay too long. I just like the idea of not having to mess with the parent/clone thing. If I was to stay with a split set, I get both parent and clone titles showing up in my game list, so if it's the clone only that I want, the parent is present, and shows up in my list. I don't want that. Also, FWIW, I'm running retropie, so I'm limited to a handful of MAME versions. I've settled on lr-mame2003 (078 romset). Also, not sure about using the mame binary since I have to run clrmame pro on a windows desktop computer, and running mame on a raspberry pi.
I will try this when I get home today, but with option A, once scanned and a list of missing files are produced, is there a way to point the rebuilder to my main folder (which contains all the required parents), then tell it to rebuild into a newly created folder?
Thanks for your help, btw.