We highly recommend you use our intelligent tools (Design->Theme->Layout, Design->Theme->Theme Settings) to customize your storefront. However, you can always change your theme file directly through "Design"->"Theme"->"Edit HTML/CSS".
To do so, you should have some kind of knowledge about html and css. Please remember, if your storefront is mis-formatted after modification, you can always rollback the changes by clicking the 'Revert' button on the top-right.
Each theme includes lots of files, but you don't need to go through all of them. Here is a list of the major files.