Generally there are 4 methods:
1) A Per-User pure package: The application and all of its resources are installed to areas the user has ownership of. HKEY_CURRENT_USER, The Users Profile, the users start menu ectera. Since you are repackaging someone elses application, this is unlikely.
2) Install with elevated privs: Since MSI runs as a service it supports running packages with elevated privledges. Many organizations see this as a big security hole so they disable it via policy.
3) Active Directory GPO: Use AD to push MSI's to collections. This assumes you have AD in your network and has limitations when it comes to scability and running programs other then MSI's.
4) Third party distribution tool like SMS, Tivoli ectera: This is the premium solution in my mind. You have a system in place with vast flexibility in terms of client discovery, organizing clients, packages for distribution and scheduling installation of the packages.