Homer allows you to define how many batteries, but I can't find a way to define how they are connected (parallel or series).
HOMER does not explicitly model the series-versus-parallel arrangement of the batteries. If you plan to use 2V batteries and you want a 24V DC bus, you'll need a string size of 12 batteries in series. That means in HOMER's optimization inputs you should enter battery bank sizes in multiples of 12.
We have given the user more flexibility than that since in many cases people are not that far along in narrowing down the design.
There is one effect of the series-versus-parallel arrangement that HOMER should model but does not: the maximum allowable charge rate. In the properties of each battery type, there is an input called the maximum charge current in amps. There are other limits to the allowable rate of charge, but when the battery is nearly empty the maximum charge current is usually the limiting factor. HOMER calculates the maximum charge power for an individual battery by multiplying the maximum charge current by the nominal voltage, and then it calculates the maximum charge power for the entire battery bank by multiplying by the number of batteries in the battery bank.