Designing The System:A car is generally a sealed box with speakers and occupants inside. A boat is more like a convertible or roadster that is open to the outside environment. You will need to determine just what your system is meant to achieve. If it is just for enjoyment inside the cuddy or for background entertainment, it will require the same thought to component choice as a car. But if you intend on having the water skier 30' behind the boat to hear the music, the design rules change. I suspect noise ordinance rules will also step up.
Like designing a system for a convertible that can be heard with the top down at 60mph, it will require power and speaker cone area to produce the output needed. This can ramp up the cost and complexity quickly, so you should take a "progressive system" approach and design based on several future upgrades to get where you ultimately think you want to be. Keep in mind that this will also impact the charging system, so think about the bigger picture at the start of the project. At each point in the installation, measure and keep a record of the voltages at each component while playing a certain piece of software. In this way, you can tell where the charging system is beginning to see the limit, so you can kick in with the battery upgrade. It will also reveal if any particular components are not getting the required supply to prevent performance problems.
We have touched on audio installation primarily, since this is the type of system that has the most conditions that affect the outcome. However, there are other system components. For instance, adding video is not hard, but connector corrosion will affect the picture far before it affects the sound. Fiber optic connections will reduce the metallic problems of corrosion, but not everything is fiber optic (especially not video). Installing a surround system in a boat is often more difficult than doing so in a car due to the placement of the multiple speakers and other attributes. Cars are fairly symmetrical, where you can install a left and right speaker in nearly mirror-image locations and even surround systems are easier in a car. An in-car navigation system would be a problem, since there is no place to pick up the VSS (vehicle speed sensor) signal that is normally derived from the wheels, axle or transmission in a car. Fortunately, there are specific marine navigation systems commonly available.
The broader physical installation is also a major consideration. Boats are pretty easy to get into, so you will need to either make visible components easily removable for safe keeping or consider some form of alarm system for a level of protection. Without doors, an automotive alarm is still the best choice, but you will need to integrate other sensor types like pressure mats and movement sensors. The equipped impact sensors will not give you much more than a lot of false alarms.
While intruders are one source of concern, the weather is another. I recall a system in my old 25' Checkmate ski boat. It consisted of a head unit, six speakers, two 12" subs and a total of four amplifiers. The system provided many hours of enjoyment. One evening, I securely tied it up on the beach near the cabin, only to find that over night the boat filled like a bathtub with water from a heavy rainstorm and wind-whipped waves. The equipment was soaked, and while the amplifiers survived, I had to replace the head unit and speakers. I was lucky it was an outboard.
Miscellaneous
An alternate battery system is a mainstream approach for a boat, where in a car the preferred approach is to upgrade the charging system via the alternator(s). Positioning the additional batteries will require that you consider keeping the center of gravity low to reduce messing up the balance of the craft.