You mean deploying the MSI via Group Policy? Extracting the MSI from the EXE installer should work. Look at the command line parameters for the installer here:
http://www.classicshell.net/faq/#install_commands . Then you should be able to use regular Group Policy MSI deployment.
Classic Shell per-user settings are stored in the registry at HKEY_CURRENT_USER\Software\IvoSoft\<component>\Settings subkeys. The various subkeys under IvoSoft called 'ClassicExplorer\Settings', 'ClassicIE\Settings' and 'ClassicStartMenu\Settings' store the settings for various components. The settings in HKCU are all per-user, so you can export and merge the regs per-user account.
Or you can enforce them for all users by storing them in HKLM\Software\IvoSoft. There is also a way to only change the defaults but for all users. Look at the Administrative Settings section in Classic Shell's help file on how exactly to add the correct values to the HKLM registry.