four channel amp to subs and 6x9's

First thing you have to do is to know why the Alpine amp isn't working anymore.  Worn out?  No, not likely.

Then you look at a subwoofer wiring wizard like this one.  Select two single voice coil 4 ohm speakers and look at the diagrams available....and the type of amplifier you can use with those available configurations.

When you say you "believe" the subs are wired in parallel, that's not good enough.  They're your subs, the amps are your equipment, and you're going through amps unnecessarily.  You have to actually LOOK at the sub wiring and make sure you know how they are connected, and what impedance load you are putting onto the amplifier.  Compare the sub's wiring configuration to the diagrams in the wiring wizard.

My guess from 500 miles is that they ARE wired in parallel and that you have a 2 ohm load with that setup.  Look in the wiring diagram and see what kind of amplifier will handle a 2 ohm load.

Don't ruin your new amp with the same hookup you used with the Alpine.  And good for you for searching out some help and asking about it here.  There IS a way to use the new amp for the subs alone, but the subs will have to be separated electrically from each other...or wired together in a different way.  Post back after you've removed the subs from the box and inspected the wiring.

And no, the stock 6x9s can't be hooked up to an aftermarket amp.  Replace them with just about any aftermarket speakers that are built to handle more power than the car's radio alone would put out.

Your two subs will wire in parallel to 2 ohms, and that is too low of a load to bridge to two channels of that amp.  I don't know what the continuous power rating of the sub is, but you could possible use just one of them and bridge its 4 ohms onto two channels of the Octane amp and get 250 watts.  If it will handle that power that might be your best solution for sub bass considering the types of music that you prefer.

If the subs handle considerably less continuous power you could wire the two of them in series for an 8 ohm load and bridge that to the two channels.  The power output will be cut....probably to the 160 watt range... but you would have an increase in db by virtue of having an additional sub in the mix, so it would come out about even either way.

Consider building a new enclosure for the sub (or subs), too.  You can learn a lot about that here.

The other two channels can power a set of speakers.  For now, you have the 6.X 9's, and the 2 X 80 watt rating of the amp is appropriate to power those.  Use the high pass filter for the front speakers and the low pass for the sub.  And it is best to allow only one frequency range to a subwoofer, as opposed to your suggestion that you might run the two differently from one another.