Netbeans sample project on how to deploy FtpServer to an application server. It is easy enough to create an Eclipse project with these files (you just copy the contents of 'src/java' directory into Eclipse's source root and web.xml to WEB-INF/web.xml.
Although I tested it with Glassfish, it should work on most application servers or Servlet containers. Actually, it seems that a bug on Glassfish 2 (according to MINA guys) could prevent FtpServer from running on Windows machines. But it is working perfectly on our linux servers.
src/java/ftpd-typical.xml should be edited to point to the appropiate keystore and user.properties files ( in resources/ users.properties there's an example of a user.properties files included in the source of Ftpserver core).