After you install and license Server components, if you select Configure Server now on the last page of the installation, the System Settings window automatically opens. If the window doesn't open automatically, select the Alteryx System Settings shortcut icon on your desktop. You can also access System Settings in Designer under Options > Advanced Options > System Settings.
From System Settings, you can configure your Server instances to be a single or multiple-machine configuration. Go to Configure Controller and Workers for more info on single or multiple-machine configuration.