toussi,

This module is designed to make a single install of ZenCart that is capable of hosting multiple site and managing them from a single admin location. If you already have two sites, you could use it, but I would suggest installing a 3rd fresh copy of zencart, applying MultiSite Module, then integrating the first two sites. Assuming you did the templates correctly on the first two stores it would be pretty easy to integrate their template info into MultiSite.