It's actually really easy to calculate things. I prefer Libelldra over Smogon myself, but use whatever works better.
Libelldra:
Atk = Attack or Special Attack of the attacking Pokemon (at the bottom the +0-6 is stage) Example: Dragon Dance = +1 Attack
Def = Defense or Special Defense of the Defending Pokemon (at the bottom the +0-6 is stage) Example: Calm Mind = +1 Special Defense
HP = HP of the Defending Pokemon
Base Power = Base Power of the move DO NOT factor in STAB Swampert's Earthquake is 100 not 150
Stealth Rock = x1 is neutral to rock and the others are weak or resistant Example: Yanmega is 4x
Type 1 = What does one of the defending Pokemon's type take from the move (Yanmega x2 for Fire)
Type 2 = What does the other type take from the move (Yanmega x1 for Fire)
Type 1 = Bug Type 2 = Flying
It really doesn't matter which order they're in.
STAB = Same Type Attack Bonus meaning is the move your using the same as one of the Pokemon's types (I'm sure you know what STAB is, just select yes if the move gets it and no if it doesn't)
Abilities = If the attacking or defending Pokemon has an ability that would somehow weaken or power up the attack, it needs to be selected Example: Intimidate/Adaptability
Items = If the attacking or defending Pokemon has an item that would somehow weaken or power up the attack, it needs to be selected Example: Life Orb/Occa Berry
Miscellaneous:
First four are pretty obvious
Weather + = Is the attacking Pokemon getting a weather boost? Example: Kyogre's Surf in rain
Weather - = Is the attacking Pokemon getting a negative weather boost? Example: Surf in Sunny Day
Rock Type = Only check this if you want to calculate how much a special attack will do to a Rock type in sandstorm Example: Focus Blast vs Tyranitar
Wait... how do we know what to put in for atk, def, and HP?
1 Stat Point = 4 EV's
Nature = +/- 10%
Lets say we're trying to figure out Salamence's Attack:
We know it has 306 Attack with an IV of 31 and a neutral nature. Lets say it has 252 Attack EV's and Adamant nature.
306 + (252/4) = 369 This is what we get if we just have 252 Attack EV's and a neutral nature.
369 * .1 = 36.9 + 369 = 405.9 = 406 (I think the game might round that down for some reason, though)
Alternatively, you could just go to Smogon and look, but if you need to do a calculation for like 100 EV's and a + Nature, you'd need to use this method.
Now that we know how to do that we just put everything in and click "Calculate Damage"
Lets try:
252 Timid Heatran's Fire Blast vs 0/0 Modest Yanmega
Atk: 359 + 0
Def: 148 + 0
HP: 313
Base Power: 120
Stealth Rock: x4
Type 1: 2x
Type 2: 1x
STAB: Yes
No items or abilities
Nothing for Miscellaneous
Calculate Damage....
It will do a minimum of 200% and a maximum of about 236% On average it'll do 217%
It also shows you the survival chances of the Pokemon if they have Leftovers and after Stealth Rock
Useful links:
Smogon /
Libelldra Damage Calculator
SandStorm percents WILL NOT be in the rectangle at the bottom, they will be above that and to the left!THIS IS ONLY FOR ROCK TYPES WHILE IN SANDSTORM
Congrats, you just learned how to use Libelldra damage calculator. Yay. I'll do Smogon's later and edit this post. xD
Edit: And he already figured it out... xD I spent so long on that. :/