Correct way to include include scripts
One way to include JS (or CSS) files, is to use the includeJsFile tag.
This tag will queue your file and append to the end of the &lt;body&gt;.
If, for some reason, you don't want this (say you want to include JQuery in the &lt;head&gt;), I would just use &lt;script src=""&gt; etc.

This might also solve your second problem.