Up to a certain release of z/OS (and I don't recall which it is), Java must be installed by your site support group; later releases of z/OS include Java as part of the system install.
The easiest way to run Java is to go into OMVS and type in java -- although it is possible to run java through batch. Your best bet to find out what is required at your site is to contact your site support group.
IND$FILE is one way other than FTP to transfer files -- cut and paste works, and there are others depending upon your site and which products are installed at it. Contact your site support group for details.