When applying a Golden Bottle Cap or Silver Bottle Cap, will the Ev's be trained as well? or is that something that the individual trainer must accommodate ahead of time?
As you said, the EVs must be accommodated otherwise. There are a multitude of ways to EV train Pokemon - these can range from defeating certain wild Pokemon or even in Poke Pelago. For a more detailed reading of EV training, check this Serebii page.