I have the same boat with the factory "upgraded" system.
Factory sub location below the captain's seat:

Factory amp location in front of the helm:

You're going to get a lot of replies saying to go with anything
but Clarion. It all depends on what you want. Can you do better than Clarion? Sure! It's just money. Me, I'm perfectly happy with the Clarion system as it is. I did buy a set of replacement Polk db651's but haven't installed them yet and frankly am in no hurry.
BTW, it's easy to add an iPod input to these boats - see the little round plug near the grab handle:

Separate subject - do you have dual batteries?
Whatever you do, you've got a great boat there... but then I'm a little biased.
