About 2 months ago, I went out to start my car and it did not start. I called roadside assist and it was jump-started at the 12V battery in the trunk? Was the correct? After that time I had codes P3003/P3006. I ended up replacing the hybrid ECU/battery pack. My 2003 Prius starts fine; however, it seems like the 12V battery is only holding a 9-10V charge. Will it charge up by driving the car or should I purchase a new 12V battery?
9 or 10 volts would indicate a severely discharged battery. That one might not come back to full health. (You could try, by leaving it on a smart charger, no more than 4 or 5 amps, for a full 20 hours or so, and see what happens.) On the other hand, yes, when you have a healthy 12 V battery there to begin with, using the car should keep it charged. You don't have to drive the car—the battery is getting charged whenever the car is in READY, whether it's moving or not—but it needs to be in READY for enough hours every week or so to keep the battery decently charged.