The amplifier running all six speakers is the way to go. If you were to run the bow speakers off the head unit then you would have to gain the amplifier up inordinately high in order to keep the head unit, with much less power, from clipping prematurely or running out of juice way before the amplifier. And that would raise the noise floor not to mention create a more narrow sweep on the volume control. In the end the head can't keep pace despite the similar power ratings.
As the impedance is lowered in the cockpit due to the paralled speakers the need for amplifier input gain is reduced. This is where you will start to set your gain. Then you will move onto the bow and match those speakers at the identical output level. Technically, once you level match, all six speakers will be getting the identical 40 watts.
And yes, set all channels to the lowest highpass setting or around 50 Hz. You will not be reducing any frequency that a 6 1/2 could otherwise produce but by limiting the amplifier responsibilty and the speaker bandwidth/unnecessary
excursions, the coaxials will play louder, sound cleaner and handle more power.

David
Earmark Marine