SCCM 2012 best practice, create an application for an msi and a deployment for an exe?`

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New to SCCM 2012 and have a lot of applications with msi's that I am creating applications for. I've also been able to create a few applications with exe's. Is the only reason to use a package, if you need to run multiple programs or apps in succession?

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One of the reasons to use a package vs application model is handling configuration outside of the MSI / EXE. Say for instance, your MSI / EXE does everything but it doesn't set any of the configuration items like the license information, or which server you need to connect to. Now most of these things can be handled via a custom action within your MST (Transform) by using Installshield, but if you have an executable it gets a bit more complicated because there isn't really anyway to "hook" into the installer to provide additional configuration items.