Let's take a 6-channel amplifier for an example. You can stretch it to all three zones (in-boat coaxials, sub and tower speakers). Two channels will bridge mono to the sub. Two channels will run up to four conventional tower coaxials.
Two channels will run four cockpit coaxials. The bow coaxials would run off the source unit power. Here are the shortcomings: Its not enough power to reach wakeboarding range with any degree of authority and without overdriving these two channels into distortion. The tower speakers, whether conventional coaxials, HLCDs or a hybrid, require a much greater level of power given the challenges than do the in-boat speakers. Any 5 or 6-channel amplifier is going to be limited to around 100 watts per channel highpass and that is simply not enough for this task. That same level of power is perfect for the in-boat four cockpit coaxials. In reality the source unit power is limited to around 12 watts per channel to drive the two bow coaxials as compared to 50 watts driving each of the four cockpit coaxials via the amplifier. This is based on rating both of these ampifiers at a similar bandwidth. The source unit is going to clip way early. This is unacceptable because when you overdrive the source unit you also distort the preouts that feed the amplifier so the entire system gets dirty. To offset this you would have to seriously gain up the amplifier inputs which would raise the noise floor, limit the linear range of your volume control and create a condition where the bow speakers cannot keep up (not even close). Alternately, you can't run three pair of coaming coaxials off two amplifier channels as the load would be 1.33 ohms which is unstable. Next, we can load a multi-channel amplifier down selectively but to stretch all five or six channels to the limit will overtax the amplifier's common power supply and you are going to thermal the amplifier on a warm summer day. Can you get by in the short term this way and build incrementally? Sure.
In the end, the most cost effective and simple amplifier division is going to be between tower (2-channel amplifier) and in-boat/subwoofer (5 or 6-channel amplifier).
Planning for this will keep you from buying something that is disappointing and obsolete.
As systems become larger the best configuration will change. If you want to dominate then the approach will change. What I have outlined fits everything from a family boat to a very impressive system and will last problem free.
From here you just need to correctly balance the amplification and speakers. A balanced design will have more to do with the performance and value than what you spend or what you save.

David
Earmark Marine