The Aimeos web shop is able to use different databases for its data domains. Thus, you can configure a separate database e.g. for all customer or order related data. If no specific database is configured for a data domain, the default database will be used.
The best place for the configuration is within a project specific TYPO3 extension. Please have a look at the article about extending Aimeos to find out how this is done. Afterwards create a file Resources/Private/Config/resource.php in your extension that will contain the database configuration. More details about the available domains and the necessary configuration is available in the
Using a separate database for the customer data is useful if you want to access existing customer data from another TYPO3 installation. This enables a "single sign on" for your customers only via configuration. But remember that the tables for the customer domain must be in the same database as the fe_users table!