I only keep a full 0.161 set and each version update pack from then on. (All stored within one directory)
What makes things easier is using the Set Information tools within the scanner result window.
I have a list of all my favourite MAME roms listed in a text file. (MAME_Favourites.txt)
On each new MAME release, I let ClrMamePro read the MAME binary to get the XML information it needs. I do a scan, and from the results page I click the Set Information button. From there you load that text file which will enable only the roms you need for those games. (You don't have to worry about CHDs, or the exact roms needed for the set, it's taken care of automatically.) From the same page, you can now export a dat file for just your mame games.
I use this dat file in ClrMamePro with the paths set to where I store the roms for Launchbox. If for some reason it's missing any roms, switch to the rebuilder which has the update pack folder as source and fixed.