Look at qa-include/qa-theme-base.php file, there are many functions you can use:
$this->head_title(); $this->head_metas(); $this->head_css(); $this->head_links(); $this->head_lines(); $this->head_script(); $this->head_custom();
$this->head_custom() is probably the best, that's the one I use.
Follow the guide here:
http://www.question2answer.org/layers.php
http://www.question2answer.org/qa/10186/how-to-edit-header-in-q2a-template
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