Hi,
I am not a big fan of Catalook (more of the opposite...) and I haven't and will not test Catalook support. But, you can try adding the Catalook modules on pages that are not under a root language page.
Such as:
fr
...Accueil
en
...Home
Catalook
...Checkout
...Product Catalog
Our extensions should still set the user language to the last user language used when accessing a page not under a language page. The Catalook language selector might not work. You can try disabling the Process Language Url Parameter option in LE to make it work, but you will loose the standard "flags" selector support on non Catalook pages.
As for menu, you can configure pages that will only redirect to the Catalook pages if you want to have the "Checkout" menu item in each language.