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For example, in my case I unchecked auto start of the tracker database, when I did a restart, it fails to relaunch saying error code 3. I want to configure the auto-start of the database again, where can I configure the database before startup?

A dbxml file for a configured connection pool in your Martini Runtime instance is located at <martini-runtime-home>/conf/db-pool/, location will differ depending whether you are using the Martini Desktop's embedded Martini Runtime instance, or a standalone Martini Runtime instance (See what the directory structure look like here). If you want to modify the connection pool's configuration directly from source, you should look for a file called tracker.dbxml in the said directory.

To have the connection pool auto-start at runtime, look for the property called autoStart and set its value to true. You should be able to have the tracker database start properly after a restart(if it's already running)