Odds are you don't have an engineering degree in electronics, and your probably not an electrician. (If you are, great - it will probably make sense to you.) Things like amp-hours, watts, mA, volts, peak power, and the like probably induce the beginnings of a migraine. Hopefully we'll be able to shed some light on the subject and give you the confidence to spec out the power requirements for your system, and give you some ideas on products that will help.
For starters, lets talk about 12 Volt batteries. The main spec on a battery that you need to pay attention to for powering fishfinders and radios is the amp hour (Ah) rating. The amp hour rating is determined by math: Ah= Amp draw*hours. So a fishfinder that draws one amp continuously for 12 hours will use 12 amp-hours of power (12Ah=1A*12h. Which is a fairly common power usage for a fishfinder).
Some batteries list this in a mAh rating, which would read 12,000mAh instead of 12Ah. Any of your electronics should have an amperage rating. For a basic installation of a fishfinder, find the amp rating, then multiply that by the amount of time you want to fish before recharge. This should give you a target amp hour rating to not go under. As you add more equipment, do the same thing taking into consideration how often you will use the device and adjust your hours in the formula accordingly. Once you have an Ah number for each piece you want to power, add them up, and this is the size battery you need if you aren't going to charge the system while on the water.
The three types of batteries commonly found today are Lithium Ion, Absorbent Glass Mat (AGM), and standard Lead Acid. Each of these batteries have pro's and cons:
pro's: small size, light weight, works at full power through most range of charge, works upside down or sidways.
cons: costs significantly more, lower Amp hour rating for size, depending on type, it may require a special charging kit (usually sold with the battery).
Pros: easily obtained and replaced, lower cost per Ah rating, standard charging system (trickle charger) works just fine, works upside down or sideways.
Cons: large and heavy, as the battery drains so does available voltage.
pros: easily obtained and replaced, lowest cost, standard charging system works.
cons: must remain upright to work right, heavy and larger, as the battery drains so does available voltage, may require liquid to be refilled. not recommended on a PWC.
For powering auxiliary fishing equipment on your jetski I would recommend the AGM batteries. The Lithium is a solid choice if your amp hour requirement is low, and budget is high. A properly sized lithium battery can weigh in as much as 15lbs lighter than an AGM or lead acid the same size. That is a huge chunk of your available weight capacity on a jetski, and worth looking at if weight and stability are pushing limits.
Now for the installation type, here you have two choices - a completely stand alone system or integrated in with the electrical of your ski, luckily for you there is no need to re-invent the wheel here with either choice. Several factors will help you determine which is best for your application; installation knowledge, cost, versatility, redundancy, to name a few.
For the stand alone - look to the kayak fishing world, here there are plenty of products and knowledge here for powering electronics on a craft without charging capabilities. Products like the Elephant case or Pelican kayak battery boxes offer a very resilient package to keep your battery terminals dry and corrosion free.
1st determine what physical size battery you need, then find the battery box that will hold it, in some instances you can purchase a battery with a higher Ah rating that is still within the same frame size, so be sure to talk to your battery supplier about the highest Ah rating for the frame size you select. This system is the simplest solution, but requires that you keep the batteries charged independently of the ski and you must fully charge them prior to use to ensure you don't lose power on the water.
For the integrated system, power boats and jetski's have been doing something similar for years, even decades. For obvious reasons it is important that your electronics do not drain the power of your starting battery below what is required to start your jetski. For really low power consumption requirements, you can just pull a circuit off your ski's start battery. This is risky, as you will need to monitor your battery charge and not let it drain too far down that you cannot start the jetski. If your only powering a small fishfinder, this option is doable, though I'd recommend having the display on the fishfinder always give a voltage reading that you can monitor. The best option here, is to install a second battery with an automatic charge/combine system.
Blue-Sea add-a-battery kit is ideal for this. This system when properly installed allows for redundant start batteries if needed, but keeps the two batteries isolated when not, it will also charge both batteries, putting priority to keeping the start battery fully charged. However, installation of this kit can be complicated for someone without electrical know-how. Unless you are very confident in your schematic reading and installation ability, you should have the work performed at a service shop.
It is important that any circuit you install is sized right, properly fused, and all terminations and splices get a coat of dielectric grease to resist corrosion. The electrical system you install on your ski needs to be done correctly, else very bad results will happen. Your extra batteries need to be mounted very securely, a lose battery bouncing around inside your ski can cause a fire that will not be able to be put out. If done correctly, these risks are mitigated and you can fish with confidence that your navigation and power systems will work flawlessly, turning heads with every netted fish!