This is an empirical article based on 10 years of cruising experience, with no technical verification.
WARNING: if you are not competent in 12 volt marine wiring practices you should have a professional installer perform this installation.
The deep cycle batteries or battery banks usually found in cruising boats were designed for deep cycling. This may seem rather obvious but it turns out that if you don’t deep cycle them you can destroy them. This is no problem when you are cruising away from shore power but for those long stays at the dock you need to take protective measures.
With a battery charger maintaining a constant voltage, those intermittent loads such as flushing a toilet or running a water pump take just a tiny charge off the top of the battery capacity which is replaced in a few minutes by the charger. This short cycle, always at the same place on the battery plates, can produce a layer which can materially reduce the capacity of your expensive battery bank and shorten its life drastically.
There are two solutions. One is to turn off your charger until the bank is about 20% discharged so that the battery is not short cycling at the same spot. This has the problem of remembering to turn it back on and also that you are using up the cycle life of your expensive battery bank. A much better solution is to completely disconnect the battery bank from your system and replace it with a regular automotive starting battery. These batteries are designed to operate in this manner and one small battery is adequate for supporting those intermittent 12 volt loads with the help of the on line charger. Now days you can purchase one for about $30.00 with a 3 to 5 year life guarantee. You probably are voiding the warranty by using it on a boat but you will be getting a battery that will support the load for many years at minimal cost.
Marine supply stores sell an economical single-pole battery switch that makes the changeover simple. Put one in series with the battery being isolated so it can be disconnected. Leave the cheapo 12 volt in circuit all the time – it adds a little extra capacity.
If your (now) isolated house battery is of the maintenance free type, it can be left idle for long periods with no significant loss of life but you should put them back on charge once or twice a year to keep them ready. If they are the lead-acid type, you will need to check the voltage more often.