The whole purpose of this mod is to manage multiple stores from ONE backoffice. This is especially handy if you share products across more than one shop.

if there are two or more completely different shops with different products
Then rather use two ZENCART installs.

3. tried to create a user in second shop with same email address but got a message that a user already exists
This allows the very usefull function of cross-shop purchasing in one shoping cart. Great future if you run your multiple sites as departments and allow customers to buy from the various departments in a single shopping basket.

I see this mod as something to be used when you sell, lets say computers, and you want to offer themed departments for your various main brands whilst sharing your common products like cables, ink and other accessories.