1) Select the game generation you are looking to battle in.
2) Choose your Pokemon from the list to automatically load it's default base stat information.
3) Input how many EVs you have available to invest (after you've determined ATK, SATK, and SPE), along with it's level and desired Nature.
4) If you plan to use any defensive stat boosting moves, adjust the bonus modifiers.
5) Decide your bias. Meaning whether you'd like to split your defensives more one way than the other (ex: Take more physical hits than special).
6) Click the Optimize EVs button and the Optimizer will calculate the best EV spread to take the least amount of damage.
NOTE: Base Stats can be inputed manually if desired. Selecting a Pokemon will autofill them with the appropriate stats for the selected generation.