1) First determine what types of batteries you do have. Starter battery can sometimes be defined by type or by function. A true starter battery type has thinner plates, and it is designed to produce high but short bursts of power. These type are not adequate for deep discharge. Their size is usually rated in CCA (cold cranking amps) and are usually labeled as staring battery. On the other hand the house batteries are usually deep discharge type. These are designed to accept multiple cycles of charge/discharge. Their size is usually rated in Amps and labeled as deep discharge. (there is a third type marketed as a dual function, an in between hybrid). The thing is that in some boats the owner could have installed a deep cycle battery to perform starting functions.
2) Do not combine a starter battery with a deep cycle except in an emergency for a short period of time. Nothing drastic would happen but it is not good for the system or either battery. If both house and starting are deep cycle types then you can combine them.( preffered combination in a basic two battery system)
3) You do not have to switch the starting battery off after starting the engine; give it some time to recharge after that initial burst of energy.
4) If you have a two battery switch with 1,2,Both,Off just remember that only the designated battery will power the loads and only the designated battery will receive charge from the engine alternator. If you wanted both batteries to receive charge from the alternator you could use the Both selection if the batteries are of the same type. Think of electricity as water that will flow from a high point to a lower one. If you combine a fully charged battery with a depleted one the power will flow from the stronger to the weaker until equilibrium is reached. Consider that this may leave you with two inadequately charged batteries instead of having one fully charged.
5) Many, in a two deep cycle battery system, just use one battery to keep the second in reserve. They alternate the use with each outing to keep both exercised
6) If you have a true starting battery and a deep cycle then you can start the engine with the starting battery, let it recharge for a few minutes and then switch to the house battery. If you want to simplify things you could also just leave the starter battery in reserve and start your engine with the house battery and continue with it. Deep cycle batteries can easily start these small auxiliary diesel engines.
7) One tip. We usually carry an automotive type battery pack for emergency starting power in case we accidentally ran the batteries down.