Well I am noob. But still you shouldnt look for books 'how to create a trojan usin java' what you should look for is 'system administration using java', 'java network programming'. Well I'm not sure about java itself, but python is a right choice for that. You see remote access trojan is almost same as remote administration tool. So innocent name for that is remote administration tool. Look and learn about systems administration. Because these guys studying powerfull shiet like controlling hundreads of servers from a single computer.
So thats my noobish attempt to point you at the right direction, by how I understand things.