Keeping your power system battery bank charged up will help you get full life and performance out of it and also make sure that there is always power there when you need it.
Whenever possible it is best to return the battery to a full state of charge as soon as possible after there has been some discharge. Power systems are usually designed to have a daily DOD (depth of discharge) of up to 15% of battery capacity. In an ideal world where the sun always shines it would be the job of the solar panels to recharge the batteries on a daily basis so that the DOD would never exceed 15%. However because the sun doesn't always shine there are times when the DOD will be higher than 15%. On an occasional basis this is ok but when there is no or little sun for long periods it is very important to have a back up system of battery charging available.
In most RAPS systems the back up is provided by a generator and battery charger. If there has been no solar input for a couple of days the generator/battery charger should be used to recharge the batteries. It is usually possible to take advantage of the fact that the generator is running and make use of appliances/machines that use large amounts of power eg. washing machines, power tools etc.
Battery chargers fall into two main types: manual and automatic. Both have their pros and cons. Manual battery chargers are very versatile but require constant monitoring to avoid over charging. With a manual charger it is possible to give the batteries a "boost" charge as supplied by most regulators in solar systems. Once the maximum boost voltage has been reached charging has to be stopped or the charging current reduced to prevent over charging which can damage the batteries. Some automatic chargers can supply a boost charge and then automatically switch into "float" mode to avoid overcharging. Other automatic chargers will only charge up to a preset maximum voltage and then stop the charging process. This is ok as long as it is not relied upon for long periods of time. Hopefully after a few days the sun will shine again and the solar array will be able to give the batteries a boost charge.
It is a good idea if there has been a prolonged period of no sun and the batteries have not been receiving regular boost charges to run the generator early on the first sunny day. This allows the bulk of the charging to be done quickly (with the combined input of the charger and the solar panels) and then the solar array can supply the final part of the charge and keep the batteries in float mode for a good part of the day until they are needed again.
Battery management systems can give a good indication of the state of charge of the batteries but should always be used in conjunction with the regulator(charge controller), voltmeter and specific gravity readings.
If in doubt: CHARGE!