In Midi terms, a Bank is an input device.
In organ terms, a Bank is a group of stops that play together. In a traditional organ they probably share an action (e.g. a Tracker action) and a windchest.
If you have more than one keyboard, or a set of pedals, available to plug into Box Of Stops, each of these will be assigned to a different bank. However there is nothing stopping you having more banks than you have input devices. In that case the 'spare' banks can be played using couplers. This is the same idea as a 'floating division' sometimes seen in a large traditional organ.
Changing bank properties
To change either the name, or the input device for a bank, first tap the spanner icon to start configuration mode, then the pencil icon next to the name of the bank.
Automatically assigning an input device
When Box Of Stops is first installed it comes with a sample registration which has three banks - Great, Swell and Pedal. If you plug in one keyboard, it will be assigned to the Great. If you plug in two keyboards and some pedals though, the input devices are assigned in order - the first keyboard is assigned to Great, the second to Swell and the last input to Pedal.
This done using an automatic assign on the bank. E.g. the Great is defined with "# First Channel", the Swell with "# Second" and Pedal with "# Last".
Automatic assign is a mechanism Box Of Stops uses to learn the input devices in an unfamiliar environment - it is normally enough to get you playing straight away.
If automatic assign doesn't guess the inputs right, or if the plan is to add and remove keyboards, then it may be better to explicitly assign the input.
Explicitly assigning an input
To lock an input device to a bank, first show the properties for the bank, then press any note on the input device. You will see the input set to the device and Midi channel that was detected.