I created my custom theme but it only works on one page

I created first of all an index page – a normal one with a header and a footer, and in this index page I added a php include to wordpress’s main index page – meaning my index.php ISN’T wordpress’s index.php. I then uploaded my header, footer, css, main image files to /wp-content/themes/custom. However, it only works for the index.php and the page.php, single.php, etc. do not have the header or the footer. Take a look at http://so-complicated.net/wonderer and just click on any entry. I’ve been tearing my hair out over this, please help me!