You might want to use some tools to diagram your database but they will not use the SQLite driver (Visio is one example of this). A work-around for this is to install an ODBC driver for such tools.
Diagramming With Visio
To diagram a database with Visio, run the ODBC Data Source Administrator:
On a 64-bit system, be sure to run the 32-bit version located here:
I also had to install the 32-bit version of the SQLite ODBC driver (see above) in order to create a DSN that Visio could use.
In the ODBC Data Source Administrator window, define a User DSN (I could not get Visio to see a System DSN). Click the Add button, select the SQLite3 ODBC Driver, then click the Finish button. In the DSN Configuration window, give the DSN a name and browse to the database file. That’s it.
Now fire up Visio and create a Database Model Diagram in the Software and Database group. The Visio Database menu will now be displayed. Choose Reverse Engineer from that menu. In the Installed Visio drivers field, select ODBC Generic Driver, then highlight the DSN name in the Data sources field. Click the Next button, then enter credentials in the Connect Data Source window (if necessary) and click the OK button. A warning window will be display indicating:
Dismiss this window by clicking the OK button. Now go through the Reverse Engineer Wizard windows and you’ll end up with a Visio diagram of your database entities.