Well first off there is something you should know. Mame's xml output has been "broken" for some time, so both romcenter and clrmamepro are going to show a dozen or more games that are incomplete when in fact they just don't have a full dump of the games yet.
To upgrade mame in the safest possible way....
(Note: Do all this within the romcenter interface)
1. DO NOT put your new roms in the same folder as your old ones. Make a new folder, and add that folder to romcenter.
2. After romcenter so it's scanning thing (the next day as slow as it is

) right click on your new folder and select "fix"
3. After that's done click the little icon's that filter the view until only the green roms are visible in that folder.
4. Now right click inside the folder to select all and then go to shell operations and copy to copy all of these files into your main roms folder.
5. Scan your main folder again, repeat steps 1-4 as needed.