if the application installer provided to you is an MSI file, then you should seriously do some additional research. best practice states that should not repackage an MSI into another MSI. use a transform (MST) file to accomplish application configuration.
how do you create a transform file? well, there are numerous tools that will help you with this. on the free side, you can look for ORCA (comes with the MS Windows Install SDK, I think) or maybe the free version of InstallShield Admin Studio (these are just a couple). Some commercially available software vendors provide branded versions of the InstallShield transform generator for free to assist with distribution of their software (Adobe has one for Acrobat, and Lotus Notes client has one too).
hope this helps.