If your keeping the stock bose system you will need something called a "LINE OUT CONVERTER". Its a small rectangle box. One end will have RCA OUTPUTS and the other end will have 6 wires. The 6 wires are:
White: + White/Black: -
Grey: + Grey/Black: -
And two solid black or brown wires: ground isolation.
Tap the white into your front or rear left speaker input.
Tap the grey into the front or rear right speaker input.
(Note) use either both rear or both front, not one front and one rear.
The grounds are used if alternator whine or "road noise" is established.
The gains on the converter are usually preset, but if not take a small philips and tighten them counterclockwise shut, then a clockwise 1/4 rotation.

Remove your factory radio, unplug each harness connected your radio. You can purchase a harness(Female End) and Reverse Harness(Male End) and make a loop to tap into; but these harness' are usually pinned for non amplified systems. So you'll most likely tap into the actual factory wiring. To determine the wires(off hand i dont know without probing) you may want to check out scosche, or metra for wiring diagrams. Or search google.

Successfully installing this will convert your speaker's output to the converters input to rca output to your amp's input.

Make sure you tap into wire before it passes through the bose amp. Hope this info helps ya.
Part will run you around $20-$25.