Generally speaking:
Stage 1 keeps the stock airbox, but may modify it. In the case of the B12, both Ivan & Dale have you add holes to the airbox lid. Exactly what the contents are vary by bike model. May contain some or all of the following: jets, shims, needles, timing advancer and/or other special modifications/instructions.
Stage 2 for some weird reason is not usually offered by most kit makers, but Dale uses this term. His Stage 2 is roughly the equal to other's Stage 3.
Stage 3 usually deletes the stock airbox in favor of pod filters. Jets and/or needles are made to provide more fuel for the more air that this setup permits. Contents will be similar to Stage 1, plus may include the pod filters.
Bandit 1200 speaking:
Ivan only offers a Stage 1 style kit. His kit seems to offer better performance than Dale's Stage 1. Dale's Stage 1 kit does not work well with the K&N replacement filter. Ivan's seems to work with it though. Dale offers two different Stage 2 kits. One (Stage 2 Modified) keeps the airbox and replaces the lid with a frame that will hold the filter in place. This one willl make the same or slightly better power than Ivan's kit. The other (standard Stage 2) gets rid of the airbox and uses K&N pod filters. This one make a little more power than the Stage 2 Modified.