It depends on where your Library project is located relative to your Project project. If they are both in the same parent folder, the src for your js could be as simple as
<script src="../Library/JS/myAwesomeLibrary.js"></script>
Meaning, go up one folder past where my current file is and then look for a folder called 'Library'. You can also use an absolute path using the address the internal browser uses - though you will have to change this for the final server. The absolute path would look something like:
<script src="http://127.0.0.1:8020/Library/JS/myAwesomeLibrary.js"></script>
Keep in mind, this may work in Aptana's internal browser, but your paths may change once you get the final server if the Library, for instance, is located in a different virtual host than the Project.