@imaddicted2u Thanks for the tag.
@jeffmurph004 That's an excellent question, as stepping into the world of a factory-amplified system like the Bose can feel a bit like moving to a new country with different customs.
Between your two options, you will want to use the speaker-level inputs from the existing Bose subwoofer. The Bose amplifier acts as a traffic director for audio signals, sending very specific, filtered frequencies to each speaker. The signal going to your rear door speakers has likely had all the low-end bass removed to protect the smaller drivers. Tapping it for a subwoofer would be like trying to make orange juice from an apple; the necessary ingredient just isn't there.
The factory subwoofer's signal, on the other hand, at least contains the bass frequencies you're looking for. While this method works, be aware that this signal is heavily equalized for the small factory sub. For a cleaner and more robust signal for your new Rockford amp, you might consider using an active line-out converter (like an AudioControl LC2i or similar) on those same subwoofer wires. These devices are specifically designed to "clean up" a factory signal and can even restore bass that the stock system might reduce at higher volumes. It's often the difference between a good result and a great one.