Hey Mark,
Welcome to the forum and congrats on the new bass (coming soon)... Plugging a cable into the 1/4" jack on the bass switches on the internal 9v power which is otherwise not connected. There's no harm in having batteries onboard as they only come into play when you use that 1/4" jack. If you don't already know, the external power supply chassis has 1/4" jacks which are the instrument's "normal" outputs, so you never plug both the multi-pin cable and a 1/4" cable into the bass at the same time.
Post pics when you can.
Jimmy J