Check in your index.php file first. The CSS file is mainly just for spacing, fonts, colors, sizing, etc. Your index.php file is what should determine WHERE it shows, just not how it looks (thats the CSS).
As for positioning, I'm more of a fan of the sidebars on the right. That being said, I've had them on both sides (like you do) and on the left side as well. It's all up to your preference! Right now I have them on the right on my site,
Intermission at Work.