The recommended place to store custom javascript files is on your FTP site (customerftp.convio.net). If you don't have the username and password for the FTP site, please contact Support (888)528-9501 opt 3.

Once the JS file is uploaded to the FTP site, the Page Wrapper can reference the file using something like this:
<script language="JavaScript" src="../js/my_scriptfile.js" type="text/javascript" />

For more information on accessing your FTP site, please see How do I access my FTP? (BB735774).