You can use a JavaScript code only in the .stpl template files of Post Affiliate Pro. Also, the JavaScript code must be included in the literal tags.
{literal}
<script>
alert('Hello, World!')
</script>
{/literal}
Usage of a JavaScript code in .tpl template files of Post Affiliate Pro is prohibited due to security reasons and it won't be changed!
Though if you needed to execute some script even in some .tpl file, then include your script via an iframe.