The Eviolite works on the actual stat, not on the base stat.
So, lets say if the Def stat (this is just an example) is 200 with 252 EVs, then it would be 200 x 1.5 = 300. The EVs you invested into your Def / Sp. Def does count.
To help you with your Eviolite Scyther, you should fully invest in HP / Speed. You don't need to invest in the Def / Sp. Def because the Eviolite boost is enough. The moveset should also be Swords Dance + Roost + 2 Attacks so that it hits hard after setting up. Jolly Nature can be used to outspeed certain threats, but Adamant Nature is an equally good choice. If you are playing OU / Ubers, Scizor is generally better. In lower tiers (ex: RU / NU), Eviolite Scyther is viable.
Hope I helped!
Source: Game FAQs , Experience