cpbackup - config?

I have just had a HDD fail on one of my servers - fortunately it was only the backup disk. This led me to do a whole lot more backups across multiple servers.

My question is this - cpbackup does a good enough job of backing up per user account info, but falls a little short in the backing up of the server related stuff.

Yes, the cpbackup script has a section in it for specific files and directories to backup as well which is a good start.

Is there a way of adding to these 2 sections of the script without it being clobbered the next time it gets updated? Ideally, these 2 sections should be either pulled out into a config file or have an extra config section added.

The main reason I am looking is that I have system files that are not being backed up - php.ini files are not there, (I run php4 and php5), modsec configs just to name a couple of critical files that would be needed to easily re-build a server.