Is there anyway to override the page template?

I've been having a bit of a structural issue regarding panels. I followed this (http://drupal.org/node/495654) tutorial in an effort to create a three column custom layout for my homepage. However, after installing a module, things started going wrong. I noticed that my column layout was appearing in the content space of my page.tpl.php template. I tried disabling the module I had just installed, but it didn't fix it. I checked disable drupal blocks/regions and clicked save. That seemed to do the trick, but then when doing other things, I noticed it would revert to the page template. Over the past few days, it has gone between being fine and taking on the page template. My question is, is there anyway to override the page template. Am I doing something wrong code-wise? Should the layout.tpl.php in the 'layout' folder be considered a page template or a node (i.e. go into the content space of a page template). Any help is appreciated. Please tell me if I should provide more info.