as a proficient chess player you must play the variations and not the other way around. Come up with ways to counter these threats and play natural moves.
Studying Chess Openings

In fact, unless you have some idea of the aims of the opening you're playing, the advice to "play natural moves" is pretty useless.
I'm not sure it's useless but should instead be stated as "follow opening principles."
I'm not going to claim opening study is bad at lower rating levels, but if you run across opening replies you aren't used to, then falling back to principles may be a good idea, especially if you don't yet fully know the ideas of your chosen openings.

Well, your primary goal right now should be to improve and learn, so what you should do is learn the principal ideas behind each opening and act accordingly. Do NOT play opening moves on auto-pilot. Think about each and every one of them, take your time in the opening. That way, even if you make a mistake (and you are bound to), you will quickly understand why it happened and you won't repeat it in the future.
Play lots of games to gain some experience. Read as many annotated master games as you can. Once you hit 1500-1600 you can also start going through games without annotations, just looking at the typical piece positioning, pawn structures, pawn breaks, attacking patterns. ... and yes - work on your tactics and endgame skills.
I have been playing chess now for a little over a year and I have increased my Rating slowly from 800 to 1100-1200. I want to really start studying openings and I have been doing so, such as ruy lopez, queens gambit etc. , but how do you combat a player who doesn't respond to your opening in conjunction with the book. Such as ruy lopez 1. e4 e5 2. Nf3 Nc6 3. Bb5 and then your oppenent doesnt continue with a normal variation. Do you continue with the ruy lopez opening or do you do something completely different. I hope I explained myself correctly.