There is a database setup procedure, in this case mostly specific to SQLObject. There's no specific protocol for how you set up an application or its database, so this remains an issue. I'd like for there to be a parrallel setup procedure, so that after configuring the application you could explicitly set it up, including having it tell you what it is going to do (without doing it).
There are other kinds of integration that are harder, of course, like permission controls, or other user data. But these are points for future consideration; even if it initially means duplication in some places, having access to a larger set of software is still useful.