If I understand it right, the amplifier powers all 4 speakers with 40 watts per channel and is two or four speaker compatible. It takes the place of the head unit's internal amp of 20 watts per channel.
I'm sure with a bit of research on how to wire this all up, you could use the rear amp to drive the rear speakers and use the new amp to drive the front and tweeter pods. Or you could just bypass the rear amp and install a whole new amp to drive all 6 speakers, depending on how many watts per speaker you want to run with.
There are so many ways you could approach it. Another thing to research is ohm ratings of the speakers and what your new amp is rated for. It affects how many watts the amp ends up actually delivering to your speaker. Furthermore, when wiring two or more speakers per channel together, depending on if you go with parallel or in series wiring, affects the resultant ohm rating. Get it wrong and you can fry your speakers and/or amp.
As a tidbit, it takes 10x more wattage to double the volume, everytime you double the volume. One of the benefits of having more wattage per channel though, is that you gain more headroom, less clipping, etc. - quality of electronics and design aside. So don't expect insanely louder volumes unless you are willing to install a 1000+ watt per speaker amp and speakers that can handle it.

Hopefully you'll find someone who has done the install already on another bike and has a recommendation or find an aftermark kit that was designed to be as plug and play as possible with your current base setup.
Good luck with the project.
