Choose Protocol - You can choose the www as it is just an alias of your domain.
In Directory - This is the directory in which you wish to install the script. If you leave it blank it will install on the root of the domain i.e. mydomain.com
Database Name - You can change it to anything you wish. Softaculous creates this by adding a few random numbers to the name of the script. You can change it for your convenience.
Table Prefix - This is the table prefix for your installation. If you wish you can keep it wp_ for this time and then use wp2_ , wp3_ and so on.
Enable Multisite (WPMU) - This is the WordPress multisite option provided by WordPress. If enabled you can create the multiple sites from the WordPress.
You can test installing WordPress on the Softaculous Demo and check if the Multisite option is the one you are looking for.
http://demo.softaculous.com/enduser/