Here are a few principles I have gleaned, from replacing batteries and electrical systems on three sailboats in the past year. I agree with what has been posted so far
1. I agree that one house bank is better than two or three. Nigel Calder demonstrates the reasons why in his book, get the book as it will help you with other issues.
2. Generally simpler is better. If you tie the house bank batteries together purely with cables and don't use a switch to link them, there is one less thing to break and troubleshoot. Try to keep things simple in general as there is less to break, maintain and troubleshoot.
3. Use batteries of the same age, size and type in each bank. if the batteries are hard to access for service you will not keep up with servicing for the wet cells, also if you will leave the boat unattended for periods of time AGMs lose charge much more slowly. AGMs can be recharged much faster. Otherwise wet cells are a better value.
4. If one of these banks is in the bow (for anchor windlass or bow thruster) make sure you know how they get charged--most people charge them by connecting them to the house bank via battery switch. This means a long run of battery cables to the bow. In my opinion, if you have a generator and use it to charge the batteries, its better to run AC to the bow and run a separate charger there, but be sure that this charger is not powered by the inverter but by shore power/generator. Its easy to let these batteries go down by inattention.
5. Its very important to have a voltmeter for each bank, or some battery monitor like Xantrex for each bank, so you know if any bank is undercharged.
6. The alternator should be connected primarily to the house bank, and then to the starting bank with a battery combiner or something like that. The archives have many discussions of different kinds of combiners. Since you have two alternators, hook up the bigger one to the house bank. Make sure the alternator sensor wire is always hooked up to the battery or that you label the switch not to disconnect the battery or move the switch while the engine is running so you do not fry the alternator. Consider a Zap Stop diode to prevent frying the alternator. Consider a high voltage alarm for each alternator, they are not expensive and will prevent frying your whole electrical sytem, batteries, electronics and lights if your alternator goes berserk.
7. If your starting bank goes dead for any reason, you will find it useful to link together the house and start batteries. Easiest is a battery switch which you should label something like "use only to jump start" or you can use jumper cables. I myself keep an extra cable in the battery box to tie them together in such a circumstance, since its the cheapest and best connection. Takes me 5 minutes.
8. Clean contacts and terminals, use battery anticorrosion spray.
9. Label everything, make a checklist and post it. Its too easy to forget what the different switches are for, or get confused in an emergency, and to forget what you have to have on in order to do X. A list of where breakers and fuses are, the size of fuses etc. can be very helpful in troubleshooting. You can ensure you have an inventory of spare fuses that could be needed. Sometimes a fuse has been installed inline somewhere and if you find it now and put it in your list, this could be a godsend in an emergency.
10. Avoid hooking items up directly to the batteries, exception are sensors and bilge pumps.
11. Solar chargers should be hooked up at a separate terminal on the batteries from where alternator or other charging comes in. Consider a way to switch off while using other charging sources as voltage coming in from them can make alternator think the batteries are fully charged.
12. Verify everything, its amazing how often people use the wrong color battery cable (black on + line or vice versa) because it was at hand