Connecting to a custom database using db_connect

[Dave]

You could approach this situation in 2 different ways:
First way is to create an API for your apps which removes the need of database access inside of vBulletin.
Second way is to initialize a new vB_Database class (refer to includes/class_core.php) with your app its database connection information. That way it should not interfere with vBulletin.