If you go into var/stash/Applications you'll see a list of your Cydia installed programs.
Inside the main folder of the program you'll see a file called Info.plist.
Open this up in the text viewer in iFile and look for the text: CFBundleIdentifier, the line immediately underneath this entry should start with com.xxxx.xxxx
For example, in the Cydia program it's named com.saurik.Cydia, which is the folder you make in /Bundles/. Although, Cydia is probably a bad example because it runs as Root and currently cannot be themed, but that's how you find the name for Bundle folders.