You can use WebDAV, which has support in the iWork apps on iOS. Setting it up used to be tricky, but I have not used it in awhile. Also, if your ISP is blocking port 80 outbound this won't work for you.
Option two is to setup a regular file/FTP server and use a good file management app on your iPad to transfer files back and forth. I really like a free app called Documents by Readdle for this. It does not support AFP unfortunately, but it does support FTP, SFTP and SMB. A lot of ISPs block the ports for SMB both inbound and outbound though, so S/FTP is really the only choices.