On the left you have all 30 'classes'. Every spec of every class is presented. In the center are your groups. I have no idea why they have this set up with 8 groups. You'd only ever see 8 groups (40 players) in AV and you have almost 0 control over the composition in that arena.
Then on the right you have the raid buffs, and a count of Healers, Ranged, Melee, and Tanks. You drag the class from the left and drop it on the raid group slot. Your count is increased, and the buffs that you have covered light up in green.
Let me pick a class/spec completely at random. Protection Paladin. There. Say you pull over a Protection Paladin and put them in group 1. Your Tank count goes to 1 and you can see Mana Restore (Judgement of Wisdom), Melee Attack Speed Slow (Judgement of the Just), and Healing Received (Improved Devotion Aura) go green. You do not get credit for Heart of the Crusader, and most Protection Paladins won't have points for it.
You will see a maybe by Attack Power and Damage Reduction. This is because the program doesn't know what you will be buffing, so it puts a maybe.
I do have a couple of minor issues with the tool.
First, Feral Druids are counted as Tanks and not melee DPS. Maybe they need to add Feral (Tanking) and Feral (DPS) because the class could be doing either. All Death Knights are also counted as Tanks. Since they are supposed to DPS or Tank out of any tree, the author decided to count them as Tanks.
Second, Protection Paladins do not get a credit for having the possibility of Blessing of Kings for Stat Multiplier. I feel they should get a maybe. If I don't know for sure that another Paladin will have Kings, I'll take it.
Dwarf Priest (excellent Priest blog by the way) also has an article on the Tool here: http://dwarfpriest.com/2008/10/08/two-tools-for-raid-stacking/, as well as discussing an ingame version through and Addon called InTheBuff.