The topic "Double-booting system behavior", http://db.apache.org/derby/docs/dev/devguide/cdevdvlp20458.html, mostly describes issues that come up if you use a JDK earlier than 1.4. Since such JDKs are no longer supported for Derby, the info about these issues should be removed. What needs to remain is that with the embedded driver, Derby DOES prevent two instances of Derby from booting the same file-system database.
The problem doesn't exist with in-memory databases – the db doesn't exist outside the JVM, so multiple Derby instances could refer to an in-memory db with the same name, but they wouldn't be the same db. That needs to be said too.
The last paragraph, to the effect that if more than one Derby instance needs to access the same database you should use the Network Server, can remain (with some edits).