blazikenlv100, PokeRus simply doubles EV gains received by the Pokemon. There are a few different ways to count, but just so long as you pick one system and stick with it, you'll do fine. I myself do a PP count on how much PP I've used for EV training, and sometimes I use my trading cards to count also (e.g. when EV training Attack, killing a Carvanha counts as 1 card and a Sharpedo counts as 2, in a string of about 100 or so).
I WISH I had PokeRus in Gen 3, though!