MCONNECT support multiple websites in Magento and customers can be assigned to a specific website in Magento. For  assigning customers to a specific website in Magento the report is used "Assign items to webshop".

Go to MCONNECT==> Periodic activities ==> Assign items to webshop

Select the web shop code to which the customer needs to be connected. 

Select "Customers" in the dropdown create for.

You can now apply a filter to select a range of customers.

Press Ok and the customer is assigned to the assigned website.