Car: spark plug wire to Distributor Cap 04 Grand Am GT?

I recently had car problems, because it was shaking pretty bad, and the engine light was on. took it to Auto zone and they told me that it could be spark plugs, specifically # 5 cylinder after changing the spark plugs, I noticed the distributor cap for #5, 2 was upside down I connected evens in the front of the car, odds close to the firewall. if the distributor is upside down compared to 1-4, and 6-3, doesn't it mean I am connecting #5 to 2? and #2 to 5 how can I be sure the distributor's output is going to the right cylinder, and would it harm the car in the long run if I don't?