1. Should I generate the packages as managed or unmanaged msi ? I need to manage them by SEPM.
Use the managed client packages to have machines managed by SEPM.
2. Is there any additional script I should use with the msi package, or any MSI switch included in http://www.symantec.com/business/support/index?pag... ?
These are generic Microsoft switch. You can use the scripts as per your requirement.
3. After the installation of the msi packages, will the packages be installed as managed or unmanaged ? how can I turn them to managed ?
If the package used is Managed it will be managed client. If you are using unamnaged package then you need to copy the sylink.xml from the managed client onto this machine to make it managed.