Check out the forums at
www.romcenter.com for more info.
Basically you will want to use Romcenter or ClrMamePro to do this. Romcenter is very easy to use, but seems to be buggy with the latest sets...clearly missing stuff it shouldn't. (It only uses 32 bit CRCs and not 64 bit like ClrMamePro).
ClrMamePro is much more advanced but definitely harder to use and VERY easy to toast your roms if you dont know what you're doing (be sure to back them up/burn them before you start playing)
There are 3 ways to store MAME roms. What people / programs call them is slightly different but here is the basics.
1) Fully merged. This is what you apparently have. Assume we are dealing with Arkanoid and Tournament arkanoid. Lets say tHey have 3 roms each, and one rom us identical. Your zip file will look something like this:
arkanoid.zip:
ark-1t.rom
ark-1s.rom
ark-1u.rom
arkt1s.rom -- Differing rom for tournament ark
This method saves the MOST disk space as only the differences in clones are saved PLUS there is only 1 file, therefore overhead of extra zips (minimum block size) doesn't steal disk space. Also you can always be sure that all games within the zip are "complete" and you never have to wonder if a zip is a clone or a parent and ensure you keep them together.
2) Fully Split. Your files may look like this:
arkanoid.zip:
ark-1t.rom
ark-1s.rom
ark-1u.rom
arkt.zip
ark-1t.rom -- Same rom from above
arkt1s.rom -- Differing rom for tournament ark
ark-1u.rom -- Same rom from above
This is the most "self-sufficient" allowing you to only keep the games you want, but it also takes the MOST disk space. One file per game and duplicate roms within the file that are already in the parent.
3) Split-Merged: looks like this:
arkanoid.zip:
ark-1t.rom
ark-1s.rom
ark-1u.rom
arkt.zip
arkt1s.rom -- Differing rom for tournament ark
This is the way you find them most of the time. This saves a lot of disk space over #2, but is *slightly* larger than #1 in space usage. Benefits are you can toast the clones and keep the parents, but also if you want any clones you have to ensure you keep the parents around.
Also note: Many times the parent MAY not be the game you are familiar with playing at the arcade. It may be the Japensese version where you want the US or World version "clone" instead. Or there may be bug fixes in later clone versions (see asteroids, defender, etc..)
I originally kept mine in Split/Merged but decided to go with fully merged instead. Much easier to keep track of changes and keep clones with parents.