Yslow recommends that you should put scripts at the bottom of the page.
Where exactly should I put them, after the body end tag?
My whole site runs in jquery, so all the javascript files are needed at the beginning. If I move them to the end, it might stop my site from working. That being the case, where instead should i put these scripts for best performance?
You should put them right before the closing body tag. Make sure your scripts are being initiated properly using
And you should have no issues.