How can I use "Click Once" & "Windows Installer(.msi)" both in Visual St

There is not model where a purely MSI installed applications can get updates using Clickonce.

You could use a MSI package to required install components on the client machine and finally as a custom action install a ClickOnce Application that can then be updated using ClickOnce.

Alternatively you can have an MSI packeage as a custom bootstrapper package to be run before your ClickOnce application is installed.

Either way the final application has to be installed using ClickOnce to be able to get updates via clickonce.