With the current ISPConfig 2.2.x versions, you will only be able to manage one server. So ISPConfig on server A is currently not able to create database on server B.
If server B is only a database server, then this should not be a big problem. I recommend that you install phpmyadmin on server B and then create the databases in phpmyadmin and not ISPConfig.
If you have ispconfig installed on both servers, you will have to create a website on server B, even if its just a dummy domain, and then create the databases on the options tab of this website. In the database creation form in ISPConfig, there is a checkbox to allow external access to this database from server A.