Usually the link to the JavaScript file should be put just before the closing body tag, so that the page is fully loaded before the JavaScript tries to run. Although sometimes there might be reasons to keep it up in the head.
This is in answer to the question in your title. I’m not sure what that question has to do with your post, though.
No. Place all of the JavaScript together in one <script></script> just before the closing body tag. Never spread it out throughout your html. Better still, put it in a separate file and link to that file in script tags that are just before the closing body tag.
Yes. You target each part of the html that you are working with by selecting the appropriate id or class name or element. So the “different scripts” won’t get mixed up with each other.