You can easily integrate your Bose amp using the speaker level outputs. The factory amp output can't be more than 15 watts tops. However, if you want better sound quality, you will need the diagrams to isolate the radio preamp outputs and disconnect the factory amp.
BTW, the factory amp should be mounted on a bracket over the glovebox, not under the console. The harnesses will all be there if the car was originally equipped with the '69 AM/FM stereo (easily identifiable by chrome pushbuttons).
The line-level output is fed from the receiver through the 9 pin connector as stereo outputs. The receiver feeds back amplified output, which is then fed to the speaker harness on the receiver after interfacing with the balance, fader and volume controls.
The factory rear speakers were chassis grounded, which is generally prohibited with modern amp designs. If you choose to use a factory amp, you will want to isolate the grounds and use new speakers to provide + and - leads for each amp channel. The kick panel mount front speakers had + and - leads, but I believe the black - leads feed back to a common ground.
