For configure a custom JAR follow this 8 steps:
Step 1: Download your jar file, you can download most jar files at getbukkit.org
Step 2: Login to your panel and select the server that you wish to change the version of.
Step 3: Click on 'File Management' in the sidebar.
Step 4: Now drag and drop your jar file in the box.
Step 5: Wait for the jar to finish uploading and then refresh the page.
Step 6: Click the three dots next to the uploaded jar file and press 'Rename'
Step 7: Name the file exactly 'server.jar' (or change the value of "Server Jar File" from Configuration>Startup Parameters)
Step 8: Go back to the 'Console' page and click start, your server will start running.
All done! Enjoy your freshly installed server jar file.