Actually you have several options - depending on what you want your setup to be and how familiar you are with phpmyadmin, etc.
I do websites for a group of independently own distributors, each with their own domain name, but all have the choices of the same products from one manufacturer, and can add outside items. Since they are all uniquely owned using the multi-store setup did not work as each store can see other stores, etc.
i have one MASTER store, that is configured the way i wish it to be, with all the products, settings, etc.
Then when I add a new distributor I use the Master to get the info into this installation.
If all your stores are "related" and controlled by the same folks you might find multistore useful.
But webdevmerc is also correct - if you do one install manually and select to not install the demo then you have a clean install, And you can add that one to Softaculous, they have a nice routine up there to add manual installs.