The application is complex because it is a collection of 4 setup.exes. One of which contains an embedded msi. My question is there any best practices for repackaging complex applications like this? At my company we have a policy of not repackaging vendor msi's. However would there be an argument for doing that here. At the moment I generally use the multiple step snapshot method.
The same best pratices you use for a Single repackage is going to be the same as a multiple. You will just need to take 4x times as long cleaning up your app. : )