Menu Styles:

Suckerfish Menu:

This menu is a Suckerfish menu system and is enabled by default but if you prefer to disable it you can set the menu to "hide" in the "Template Configuration" located in the index.php file. Set the menu style to "module"   $s5_menu_style = "hide"

Top Menu:

This is the horizontal menu located at the very bottom of the page in the demo , create a “Flat List” menu module, and set the module class suffix to "-top"

Bottom Menu:

This is the horizontal menu located at the very bottom of the page in the demo , create a “Flat List” menu module, and set the module class suffix to "-bottom"

Template Configurations:
You can easily configure this template with the below options. Once you have installed this template login to the administration of your Joomla site. In the admin navigate to your Joomla templates from the top menu: Site > Template Manager > Site Templates. Select "yourstore" and then click "Edit HTML". You will then see something similar to the following:

// What color style you would like to use. Refer to our demo page at http://demo.shape5.com for a full display of styles. Enter color1-10.
$s5_color = "color1";

//Would you like to enable the popup user position box found at the top of the page? Enter yes or no.
$s5_box = "yes";

//Would you like to enable the horizontal suckerfish menu system? Enter show or hide.
$s5_menu_style = "show";

//Would you like to enable the top tab that jumps the user to the top of the page? Enter show or hide.
$s5_top_tab = "show";

Be sure to check the tutorials on the demo for more explanations and examples.

If you still aren't sure or have any more questions don't hesitate to ask on the forum.