This thread is resolved. Here is a description of the problem and solution.
Problem: user has a site with 3 languages in different domain. Now he wants to add 3 more languages under directories
Solution: currently it's not possible to do it, you need to choose only one URL format and stick to it. There are 2 options: 1. set up a multisite and create one site for each of your existing language, each with its domain, and install WPML only on the site you want to use the language directory.
2. create a WordPress install within the main site and install WPML in there. You'll end having 2 sites, one yourdomain.com where the other languages are for example yourdomain.it and yourdomain.es and one yourdomain.com/fr (fr will be the name where you install a new WordPress instance) with languages for example yourdomain.com/de and yourdomain.com/ru
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