I’m an InstallShield noob looking for help with a similar problem, but for your needs a Basic MSI Project should be sufficient.
If you are using the Project Assistant wizard, when you the get to the Application Files section you drag-and-drop your various folders and the setup.exe into the INSTALLDIR folder in the wizard and that’s pretty much it, I think.
As I recall from other issues I had creating a non-installing MSI of SQL Server, Install Shield will automatically recognize your setup.exe and run that when the .MSI is run.