>How do I calculate when to upgrade alternator?
If your battery is going dead while you are running, or they don't get fully recharged during the length of your ski runs then you need more output from the alternator. A good sanity check is to carefully watch the battery voltage. If you can read your dash volt meter well enough that's fine, otherwise put a digital multi-meter right on the battery.
If you are at wakeboard speeds or higher and the battery voltage is above 13 volts then you are doing okay. If the voltage is 12.5 to 13 volts, and your batteries were seriously discharged AND you are running a lot of stuff (stereo, ballast pumps, etc) then you are okay but marginal.
If the voltage is less than 12 to 12.5 volts you aren't charging the batteries and unless you reduce the load (turn off the heater, lights, ballast, etc) you will eventually end up in trouble.
If the voltage is less than 12 volts you won't be running that way for very long.
>When to use blue tops, when to use red tops?
The red tops can deliver higher peak currents for starting purposes (see the chart here: http://www.optimabatteries.com/publish/optima/americas0/en/config/product_info/automotive/starter.html
I would recommend using the blue (deep cycle) because your boat probably isn't going to need the extra surge capability of the red top. You need that extra current when encountering a "hard start" situation, like when you are at 9000 feet elevation and your car has been sitting all night in 20 below temperature. Since I don't think you will be using your boat in such conditions it is safe to assume your starting conditions won't ever be too bad.
What you are likely to do is run the battery down (deep cycle) running the stereo.
>Can I use red with blue?
If you are going to keep the two batteries separate, always using the red for starting and the blue for the stereo, yes. If you are ever going to put the battery switch in the "BOTH" position and leave it there then I wouldn't recommend having two different battery types.
>Is there any reason to use red with blue? (one >battery for stereo system, one for cranking)
As I said above, having one of each is fine IF you keep them separate. If you were likely to encounter a "hard start" situation then that would be the way to go.
I recommend running only the deep cycle batteries (blue top). They will provide adequate current to start your engine and they will tolerate the deep cycles you are likely to throw at them a lot better.
>Can/should I use my old battery with new
>battery (not in parallel)
Ditto what I said above. It is okay to do IF you keep the batteries separate. If you ever combine them then you have an "unknown" situation. It is even more important to not combine two different types of batteries, such as a flooded lead acid and the AGM (Optima).
>What does it mean to be marine rated
>batteries/alternators? Does it really matter?
For a battery it means it has screw post on top with a wing nut, and often also means it is a deep cycle battery. There is no reason to run use a "marine" battery.
For the alternator and many other components of the engine electrical and fuel systems the "marine" rating is MUCH more important.
On a car, any spilled/leaked fuel drips out on the ground. Fuel vapors, which are heavier than air, also flow down to the ground and can drift away. On a boat, the hull traps the vapors and can easily create an explosive mixture.
The marine rated electrical/fuel components are designed to provide an extra level of safety. Fuel systems are built to be more resistant to leaking and if they do leak to spill it either overboard or into the engine air intake. Electrical systems, especially the starter and alternator, are designed with a flame arrester.
Many people erroneously believe that the marine alternators and starters are "sealed". This not true, as doing so would block the cooling they require. What they do have is a flame arrester screen over the air vents. While the screen may look like it is useless it is actually a very viable device. Fuel vapors WILL get into where the brushes will arc, and they will get ignited. The difference is that the volume inside the alternator case is sufficiently small that the "explosion" is very small. When the flame wave front hits the screen its thermal mass cools it down and it will not ignite the vapors just outside the screen. It works.
Installing a non marine alternator or starter in your boat removes half your safety factor. If your fuel system springs a leak, or you carry a gas can that leaks, or the gentle breeze blows the fuel vapors into the boat on a fill up then you have all the ingredients necessary for a disaster.