I have yet to find a horizontal pages plugin that (a) allows you to use multiple copies and (b) merges with the themes CSS flawlessly.
With that in mind the easiest way I can think of is to do it manually:
1) create two new widget areas in the header like this in ATO->Style & Edit HEADER AREA->Configure Header Area
HTML Code:
%pages <?php bfa_widget_area('name=page_bar_1'); ?> %logo %bar1 %image %bar2 <?php bfa_widget_area('name=page_bar_2'); ?>
this will create:
a menubar
a widget area
the logo
bar1
the header image
bar2
second widget area
2) go to your site and view your home page - then view the source of the page, copy it and paste it to a text document
3) find the section starting with '<div id="menu1">' copy that section till you find it's matching '</div>' and paste this in a new text document. - You now have the code that makes up your menu. Make two copies and edit them so you have your two menus (i.e. edit the first copy so it has pages 1, 2, and 4 and then edit the second copy so it has pages 3, 5, and 6 - someting to that effect)
4) go to WP dashboard->Settings->Widgets and add a TEXT widget to both new widget. Copy the code for menu1 in to the first new widget area and save it. Copy teh code for menu2 into the second new widget area and save it.
5) go back to ATO->Style & Edit HEADER AREA->Configure Header Area and remove '%pages'
That should be it, you should now have two menubars and it will carry over on theme updates
HOWEVER - If you add a new page you will have to manually update the code to add it to the menubar you want it in. Same thing if you remove a page, you will have to remove it's corresponding code from the widget