You should read some more information on relational databases. Then think about it a bit more. You do not need to create separate databases, nor separate users. You should have one users table, each user having a primary key id, and then other tables representing other bits of data each have an owner or userid column (whatever you want to name it), where each row puts the ID of its owner.
For example, if you want to store a player's inventory, you'd have a table called InventoryItems, and columns "id, userid, itemtypeid, numberOfItems". The itemtypeid is the ID of a row in the ItemTypes table, with columns for things like image, name, stats of that type of item. Then each item in an user's inventory has one row in that table.
This is pretty basic database design and I think you are much too accustomed to flat files. So again, I urge you to read up more on your database system and relational database design in general, to learn techniques such as one-to-many relationships, many-to-many relationships (via linking tables), things like that. As you read, you will probably have many "ah-ha" moments where you think of new ways to solve your problems.
Or, you know, go back to flat files. That would work too...