When I did mine, I bypassed the Boss amp and installed my own amplifier. If I remember correctly, it was four channels. Basically front, rear, left and right. The rears have the woofers in the doors and the fronts have the tweeters along with the mids. There is also four discreet balanced line level channels that come from the head unit so your amp will have to be compatible with that if you replace it. Otherwise pull the signal from the rears for adding a sub.
Mine is cobbled together with my own parts and an amplifier module so nothing I would recommend copying. I kept the oem speakers. With the right amp they can sound pretty good.
Another issue you might run into is there is no "power on" wire like some of the earlier years. It uses a can bus or one of the other communication protocols to wake up and put to sleep the Boss amplifier. I pulled power from the RAP terminals under the driver foot well to turn on my amp