Note: Make sure you already have Bukkit enabled on your server.
1. Find the plugin you like on the Bukkit Plugin List page.
2. Download the plugin to your computer. If it's a zip file, extract the contents so you can access the jar file.
3. Login to your control panel
4. Stop the server (recommended)
5. Click Files
6. Click FTP File Access
7. Click the login button
8. Click upload
9. In the Upload to directory, click the list button and double click plugins, then click choose
10. On the left side, under the Files to upload, hit the browse button, find your .jar plugin and insert it there
11. Click Submit
12. Restart your server
It is best to upload plugins one at a time, as they can sometimes conflict with each other.