I am certainly no expert either, and I'd hope that a real expert would give you some more technical advice in addition to my reply........ but I have created several packages using the InstallShield Repackaging Wizard. (I'm not sure if your product differs) But I can run the installation using the Snapshot method, and before you actually Build the package in the Repackaged output section, you can modify the installation, such as remove shortcuts, putting in passwords, DB settings, turning off functions, etc.
Then when you have it the way you want it, you Build the package. More often than not, InstallShield will package all of the changes you have made after the initial installation had finished. Hope this helps, if not, someone should be able to give you a more technical reply.