Start by learning a little bit about DotNetNuke skins by reviewing
Lee's wonderful tutorials (scroll down on the page to find the tutorials about skins) on this subject.
Then, you should be able to take the skin that you've purchased and modify it to your liking. I would do this by making a copy of the skin's .zip file and working with it rather than the original. Once done, you can upload the modified skin to your site and use it.
Here is a more direct answer to your question: YES! You can modify your skin without modifying core code. The skin is a "template" for how a page should look. Making the modification to make the panes symmetric should be quite easy, once you understand how panes work.