The factory amp in my boat is a good one, it is a Kenwood KAC-648 I have one in my truck as well. The factory setup (I think, mine came with tower speakers) was two channels with two speakers in parallel and two channels to the tower speakers. This runs the amp at 2 ohm on two channels which it is not supposed to do, but it does. I do the same with a 2 ohm JL sub in my truck configured the same way. It will get hot and cut out if you run it wide open, but it is a surprisingly powerful and durable amp.
I LOVE my polk momo 6.5's, I highly recommend them. They have held up perfectly for three years, they sound great, I love their tweeters. They fit right in the factory holes, though I did use a sanding drum on my drill to open the back ones up a bit. Holes lined up, for the most part. I had to redrill one or two upfront, but no cutting. You have to mount the crossovers, I usually cut squares of MDF, paint them black, and staple a short velcro strap on there. Then, I glue (liquid nails) it to the hull in an inconspicuous place. It's better than wire ties. I'll post a pic of one soon. I use them to hold all the wiring that I put in, which I keep totally separate from factory wiring.