Storing Portal data in Apache Derby database works if your using standalone development environment but if you want to use clustering or if you want to support more users you will have to migrate your data from the Apache Derby database to some other production quality database like IBM's DB2 or Oracle.
The WebSphere Portal allows you to split the database into different doamins. In this each domain contains data that is related to each other and has specific characteristics about growing. Following are the database domains
Websphere provides you to very flexible options for managing these data. Either you can create one database and store all the data in it, in which case each of these domains would be stored in separate schemas or you can store say Release and Customization data in DB2 and rest of the data in Oracle.
On my local i am using one DB2 instance WPSDB and storing the different domains in there own schemas. Take a look at screen shot of DB2 Control Center