Theme Customizer should be active on your theme already. When you click Customize, you should see the header options in there. To add a new section that allows custom logo upload, try something like this
Add this code on function.php
https://gist.github.com/c2975a7a17df24705e99
Then add following code in to your header.php file
<img src=”<?php echo get_theme_mod( ‘alts_logo’ ); ?>”>
