First, Atar is a rank. You are ranked in comparison with the rest of the state.
As you're doing 6 subjects, your Atar will be calculated by:
English/Lit/Eng Lang. (Has to count in your top 4 no matter what)
You're next best three scores
And then 10% each from your lowest two scores.
So let's put that into practice. Say if you were to score 40 in all your best four subjects that would mean you'd have an aggregate score of 160. Say your lowest two scores were 35 each then that would mean you'd receive another 3.5 aggregate points for each of those scores.
So together that would mean that you have an aggregate score of 167. 167 would roughly equate to about a 93 Atar.
Note: For the purposes of this demonstration I didn't say which subjects and whether they scaled up or not. (That's something that shouldn't be in the back of your mind anyway though).
So basically Geography will count but assuming you score higher than the score you got in Geo in the rest of your subjects it will play a very minor role in your atar score.
You could however do a 7th subject which would erase your Geo score (as a max of 6 are counted toward the atar) but I'd strongly recommend against this as it will only put a heap of pressure on you will make your work load so much harder and difficult.
Hope that helped and I wish you the best with yr 12

EDIT: Scaling shouldn't be in the back of your mind - At all. Do subjects you love and enjoy.