Did you see this showcase example?
Complex layout showcase example
Also, look at the very bottom of the page and click on the source code hyperlinks at the bottom of that page. Develop the same content/pages you see in showcase, get that working, and then develop your app, accordingly.
I know we are discussing PrimeFace Extensions pe:layout, but Cookbook discusses PrimeFaces layout, so you can start there first, to get a working 'complex' layout working, and then you can go forward and add 'complex' layout to your app.
You apologized for the growl... i 'think' i have spent more days than you trying to get PrimeFaces layout to work as designed/expected in my app (months ago), and recently, I spent days to 'try' to get PrimeFaces Extensions waypoint to work, but I gave up and i don't think you heard me complaining in this forum.
When I migrated from p:layout to pe:layout, wow, it was quite easy, I think it took 2 days as I had to learn how to 'successfully' update content 'inside' of layoutPane/layoutPanels correctly via AJAX. The p:layout section in PrimeFaces user guide is definitely enough documentation to show you how to correctly/properly/successful add layout to your app, and how to update/manipulate content in your app.
PrimeFaces Extensions pe:layout showcase examples? plenty there too to ensure success on your part to add pe:layout to your app. Because of p:layout and migration to pe:layout, I now have nested layouts, and I 'now' know how to successfully update content inside of layoutPane/Panels.
Oh, when I spent days on waypoint and finally realized that waypoint does not even meet my requirement, so I ditched the idea to add waypoint, and just added a nested layout instead, and now I'm happy, and more flexibility for enduser to navigate through the app with less clicks, because I added menu in west, moved the existing commandButton/Links in center-north, and the existing dataTable in center-center. The outer layoutPane has main menubar in north. I shared all that code in a separate topic.
I did 'not' have to worry about this menuBar overflow in fullPage-layout issue that you're having, when I migrated to pe:layout, because I had menubar overflow in fullPage-layout working when I added (PrimeFaces) p:layout to my app some months ago.
I'm loving PrimeFaces and PrimeFaces extensions!