It took me a while to get this package to work so I hope this helps others.
First you will need to download the CuteWriter.exe and converter.exe from CutePDF. The former is simply downloaded from their downloads section but the later can be found at http://cutepdf.com/download/converter.exe.
Converter.exe is an archive that you will need to open and extract the contents to its own directory. I use 7zip to accomplish this.
Once you get to the Select Package section of the Package Wizard change the type to Command Line Installation (.exe). Click the "I already have the content for the package locally on my network" radial button and click the folder icon on the right. Browse to CuteWriter.exe and select it. Select Binary Language as English. Enter /very silent for the Command Line parameter. Everything else is fine as the default.
Next click the "Use the Package Boot Helper program when performing installation of the software" check box. Click the shield icon on the right.
Remove all the enteries on this screen. Click the add action under before applying package. Make sure this action is enabled and put setup.exe (this refers to the GhostScrip installtion file) into the program name. This package will display a command prompt box when executed, but in my testing it's very quick and hardly noticable.
Under the Apply package section heading you'll see CuteWriter.exe and the settings will reflect what you have entered on the previous screen. (Mine shows packageboot.exe after coming back to it for this tutorial, not sure why but it works).
Once back to the previous screen click the Paper and Pencil button on the right next to the additional files label box.
At this point you'll see CuteWriter.exe, packageboot.xml, and packageboot.exe. You'll notice that CuteWriter.exe has a blue square with a white i in the corner of it. I removed this file and added it back in, but I'm not sure why it worked after I did that and only after I did that.
Next click Add Directory Content button at the top and browse to your directory that holds the content of converter.exe. Select the directory and click OK. Click Next.
Finish your package rules and you should be able to publish and install on any clients. I used simple rules for the prerequisite rules making sure the clients are XP sp3 or greater and 64-bit since that's the version I wanted to install. My Applicability Rules check for the absence of a registry key at HKEY_LOCAL_MACHINE\Wow6432Node\GPL using 32-bit register since it's in wow6432Node. The Installed rule checks for the presence of the registry key mentioned previously.
Hope this helps!