Inside your qa-theme/themename folder there is the file qa-theme.php which you can modificate to feet your template needs. However as Scott commented you have to take a look at the docs here: http://docs.question2answer.org/themes/ as you can easily break your site if you dont exactly what you re doing
Just a quick tip FYI. If you want to add a new div you can do it this way:
$this->output('<div class="your_class">YOUR CONTENT GOES HERE</div>');
PS: Q2A is a very good platform but requires some practise to get familiar with the way it works. Beside that, the community here is very helpful and willing to help (including me ;) ).