Dear Erdoğan Uğuz,
If in your service each customer's infobase has its own configuration copy, in general, you have to update each configuration one by one on the server side.
In 1C:Subsystems Library, there is a functionality that enables you as a developer to let your customers to update their infobases' configuration from the client side . In other words, a customer will be able to see a notification that there is a new version, click Update, and thus update only this customer's configuration.
Another approach is to use one infobase for all customers by using the data separation mechanism. Each customer may think the customer works with a separate infobase, though indeed they all work with the same infobase but have access separation to its data. In this instance, you update only one database configuration at once for all your customers.