Mike explained it very well.
Here's a little background.
Blue Sea originally recommended that a single bank charger feed the auxilary battery and that the starting battery would be maintained through the combined relay. But they didn't envision these Add-A-Battery kits being used for more than light instrumentation, such as a chartplotter/fishfinder/GPS/etc. They never used the kit, for example, as a link to combine a large capacity trolling motor bank with the rest of the charging system and they didn't envision the inequity in battery banks as applied to large audio systems. So, even Blue Sea has modified their recommendation to address what we have been doing for many years now.
If you followed the Blue Sea instructions, which is certainly understandable, then we can give you simple instructions for the mod so that a flip of the switch will give you total dual-bank isolation while in storage.