First right click the PwnageTool.
Second, Click "Show package contents
When the Folder opens, Navigate to Contents>Resources>InternalPackages

Create a new folder and rename it to whatever you want.
Open the folder and create a folder called "files"
Inside here, anything you put that relates to the firmware's filesystem will be added to the firmware. (Ex : Creating files>Applications>chat.app will install the mobile chat application into your firmware. For roms, it would be files>var>mobile>Media>ROMs>GBA,NES...etc. (You have to make these folders inside your bundles))
Next, you need to actually tell the PwnageTool that you have made your own custom package. To do this, you need to create an Info.plist telling the program what to do. You can do this by taking this "clean" Info.plist and adding the information you need to :
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>Commands(Only needed if you need to chmod or set permissions for a specfic file)</key>
<array/>
<key>Description</key>
<string>XXX XXX XXX(What the description will be in the pwnage tool)</string>
<key>Identifier</key>
<string>com.XXX.XXX(not really sure what this is for, works even if you don't have one here)</string>
<key>Name</key>
<string>XXX(What the bundle will be called inside the pwnage tool)</string>
<key>Size</key>
<integer>XXXXX(The bundle size in bytes)</integer>
<key>SupportedFirmware(Pretty Obvious. This tells the pwnage tool which firmwares can use this bundle)</key>
<array>
<string>iPhone1,1_1.1.4_4A102</string>
<string>iPod1,1_1.1.4_4A102</string>
</array>
</dict>
</plist>
Now Save that in a text file and rename it to Info.plist. Edit it to your liking to get your desired result. Once it is saved as Info.plist, navigate to your folder you created and drop the Info.plist next to the files folder (not inside). When you have added everything, rename the folder you created to (insert name here).bundle.
If all works, you should see this when trying to install custom packages in the PwnageTool.
If my explanation of the Info.plist wasn't clear, here is an example from my AppPack bundle :
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>Commands</key>
<array/>
<key>Description</key>
<string>Applications that are useful!</string>
<key>Identifier</key>
<string>com.TIMBO.apple</string>
<key>Name</key>
<string>AppPack</string>
<key>Size</key>
<integer>18224179</integer>
<key>SupportedFirmware</key>
<array>
<string>iPhone1,1_1.1.4_4A102</string>
<string>iPod1,1_1.1.4_4A102</string>
</array>
</dict>
</plist>