I'm using InstallShield 2011 to create a install package. When I install package in windows server 2012, DefaultAppPool is not overwrite and name of website display incorrect.
Example: - In IntsallShield: I config name Website is "Shopping" but when I install complete IIS is display name "Website2"
I would recommend using Wix (free and open source) if you need detailed control of the installation of IIS applications.
It has a learning curve. Please see this answer for some quick start tips.
Some further links: