Eshop also has the feature to synchronize Joomla Users and its Customers by a plugin called EShop Users. This plugin is included into EShop package since version 1.2.10.
If you are using older version of EShop, just need to choose plg_user_eshop.zip in the package to install it as a normal plugin in Joomla. If you are installing a fresh latest version of EShop, then it has already had the plugin is installed. After installing, you should go to Extensions -> Plugin Manager to filter Joomla - User plugin and enable it. Now, if users register via Joomla, they will become customers in EShop and vice versa.
EShop has a tool to migrate users from Joomla into customers in EShop. Go to EShop -> System -> Tools, then click on Joomla Users button, the system will do the migration automatically and show you the successful message once it is done.