First, IMHO, gel batteries are the worst of choice—very sensitive to charging, very intolerant of overcharging, don't charge any faster than wet-cells—stick to either wet cells (less money, more maintenance) or AGM (more expensive, less maintenance).
BTW, batteries that have sat six months without charging are probably dead. The exception to this is if they were fully charged AGMs... they would probably be okay. This is due to the fact that all batteries self-discharge, but AGMs do so at the lowest rate of the three and all batteries start to sulfate if they are left in a discharged state. The warmer the temperature, the greater the self-discharge rate, and the faster the batteries will sulfate.
First, figure out what you need in terms of battery size by doing an electrical budget of how many amp-hours you use on average—one for at anchor, one for under sail at night—and take the higher number. Then figure out how many days you want to go without charging the batteries... multiply the days by the total daily use. Double this and that will give you a rough battery bank size.
If this battery bank size is too large/expensive to fit your boat/budget...then you need to either go fewer days or use less electricity per day.
The house bank should be as large as possible, since this is the most efficient use of the batteries and they, if maintained properly, will last longer. The starting bank should be enough to start the engine properly.
The charging system should be sized for the house bank and based on what the acceptance rate of the battery bank is. AGMs have a much higher acceptance rate than do wet-cell batteries. Wet-cells are limited to about 20-25% of their amp-hour capacity for bulk charging.
The starting bank should be charged off of the house bank. Ideally, this would be by using a an echo charger, but a battery combiner would also work.