I think I have this figured out,
In order to effect change to a secondary store, you must apply a DIFFERENT template to that store, then use LAYOUT section to change that template.
I am not sure about your install, but mine does not list the Default_html5 as an installed template, so it made this VERY confusing. The lack of documentaion did not help, but I digress.....
First read this post
http://forum.abantecart.com/index.php/topic,1340.0.htmlFollow it excactly, name your new template for your new store, then make changes to template, and APPLY it to new store, done....
I am still having issues with some content NOT holding per store settings, but overall a very usable setup.
Hope this helps someone ! It would have saved me a day !