The setup you want will give you three isolated installations. The benefit of using WordPress Multisite is that from one login you can access all three sites, also it allows you to do upgrades and control the plug-ins and themes for all the sites. Basically it’s like having your own wordpress.com. Now depending if it is a new install or not it will define your structure.
Please refer to the WordPress Codex for more details: https://codex.wordpress.org/Create_A_Network
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