Justin- You have come to the right place for help and info on installing a system in a ski boat. Don't know if you are familiar with some of the systems on this site, but let's just say they are "Olympic" level systems! The best of the best in other words!
As for your amp placement, put your amp on your port (passenger) side. If anything needs protection, it's your amp(s). The port side is a good place for a sub, but behind or in the kick plate at the drivers feet would be a better place. All depends on your boat. I've never heard of your boat.
As for speakers, just like what was mentioned earlier, don't go with marine specific speakers. But DO go with a marine deck! As for the speakers, poly car speakers are the choice to go with. Not much different than marine speakers, just cheaper and you get more performance. Anyone who tries to tell you that you have to go with marine speakers, just send them over to WW and they will get schooled. I have a sizeable system in my boat that I am very proud of, but I will be the first to admit that my knowledge in stereo installations in a boat only amounts to about a half an ounce compared to others on here. On the speakers, go with a good quality poly speaker. Don't go cheap, you WILL regret it! Unlike a car, our boat are an open air environment. Speakers in cars sound great due to they are in a sealed enclosure, the car! Our boats are open air so we have to push alot more watts to achieve a loud environment, especially when going 22mph in an open air environment. Personally, I run Focals. A little pricey but they sound amazing! Everyone will have thier own opinion on this. Take the brands that everyone suggests and go listen to them all yourself! Some like a really clean sound (Like myself), and others just want it to be louder than a train wreck.
As for the tower.....DO IT!!! Boarding to music is an experience! There is one draw back however. I have a guy in my crew we call "Militia", he throws a backroll. As most know, when throwing a backroll it takes concentration, setting it up and edging just right to get the speed and then throwing the roll. Militia has a problem behind my boat. He has A.D.D. So, when he's behind my boat enjoying the tunes, he edges out and then forgets to concentrate on the trick because he's so into the music! Now, if you have this problem, then maybe tower speakers aren't for you. LOL!!!
And as for a deck, go with a marine deck in this situation. Marine decks have a coating on their circuit boards that protect them from the elements. But more importantly, marine decks have the connection for wired remotes. Some manufacturers may offer non-marine decks with this option. Do the research though.
Just my $.02.......or $100.02!