It's easy to get confused and even some online retailers get muddled up! OTR is one example - they kind of imply that if you fit the side cover (with no other changes) this equates to Stage 2 (which it may well be equivalent to), but that isn't what a Stage 2 set up actually is.
Anyway, here's a rough guide (in pictures) that hopefully helps:

= Stage 1

+

= Stage 2

+

+

= Stage 3
Notes:
Removing the snorkel effectively does the same job as fitting the Stage 2 DNA airbox top.
There is also a restrictor insert you can fit in the Stage 2 top cover to effectively make a Stage 1.5, which would be as far as you could go with out modifying the fuelling to suit.
Here's the comparisson of air flow so you can see what each one achieves...