Put the .exe into the Files directory. Then use
Execute-Process -Path "$dirFiles\CitrixWorkspaceApp.exe" -Parameters "/silent /includeSSON /AutoUpdateCheck=disabled"
in Deploy-Application.ps1. More documentation can be found inside the PDF that is included in the release or we have a wiki https://github.com/PSAppDeployToolkit/PSAppDeployToolkit/wiki
You can also take a look at community made guide: Great beginners guide to PSAppDeployToolkit