In order to make changes to the PortaBoom image, you'll have to remaster the CD image, and add the stuff you want to it.
One thing about adding things to the CD image, your system will pause during CD reads, so if you are in the middle of a hot and heavy Doom game, and a CD read takes place, then your game will stop until the data is all read in. My suggestion would be to add the bare minimum to the CD image, and use PortaBoom Shares to use files off of another server. PortaBoom can use Shares from Windows servers (using Samba software), or from Unix servers using NFS.
Here's a partial list of tools that I used to build the PortaBoom CD image:
mkisofs for building the CD image
cdrecord for burning it
Extra programs have been added to PortaBoom that are not included in a standard Debian Woody install, see the PortaBoom CREDITS file for more details on specifically what is included.