The Link 2000 has a provision for two battery banks. If wired properly, you should be charging directly to each battery.

If you use one of Yandina's COMBINERS, there is no voltage loss. Also, you really should link the two banks using these by wiring them to interconnect the banks (regardless of the battery switch position). http://www.yandina.com/ There used to be "Pathfinder" unit, it was 3-4 times the price and didn't hold-up. You used to be able to get Yandina also from Defender and some other providers. It's easier to get it directly from them. The units come with a lifetime warranty -- and a voice on the line or someone who responds to emails. :^)))

Most people use the Battery One and Two together when using an inverter that is loaded-up for a variety of reasons. If you have a starter battery, then it really makes sense to keep the battery bank as large as possible.

In my opinion , the principal reason to keep the battery switch for Bank 1 and 2 is that if you have a bad battery, you can immediately isolate the good bank. Then you can disconnect the bad battery (if it's a two, or more, battery bank).