Can I license my setup/installer program?

No, the setup or installer program should not be licensed. The license functionality needs to be enforced when your application runs, not just the one time your application is installed. If you only enforce the license check on the installer, the user could freely copy and use the main application on other computers after the installation.

When using the Instant Protection PLUS 3 wrapper, wrap your application file (such as an EXE or DLL), and then package that wrapped file into your installer.