When using a Software Deployment Tools such as Tivoli, SMS, ZenWorks or similar, all you need to do is mimic a manual install as documented here: Setting up Your First HCL Notes Client with panagenda MarvelClient.
1.) Put/replace the MarvelClient binary in the IBM Notes program OR data directory. For multiuser clients, the binary can alternatively be put in the common(!) data directory (e.g. C:\ProgramData\IBM\Notes\Data\Common)
NOTE that for IBM Notes releases 10.0.1 and up, you do NOT need to deploy any binary, but would rather use Administration\DLL Updates to deploy newer or licensed binaries:
Don't forget to then also check the option "Always detach binary/"DLL" to Notes data directory" as your end users usually do not have write permissions in the IBM Notes program directory.
2.) Adjust / add / replace the Notes.ini-entry EXTMGR_ADDINS=
3.) If you did not install the MarvelClient Config database in the default location (panagenda\pmc_config.nsf for MarvelClient Essentials, panagenda\panagenda.nsf for panagenda customers), then also set MC_DB= as needed
4.) Optional: Add any additionally desired notes.ini entries
All in all, the deployment with software distribution tools is very easy, because no changes are required to IBM Notes client shortcuts (i.e. Windows desktop shortcuts), but only one file with a few notes.ini entries needs to be deployed.