create a script file on the unix box.
FTPfiles.sh
-------------
#!/bin/sh
ftp -n ipaddressOFwindowsBOX << EOF
user ftpusername ftpuserpwd
put nameOFfile
EOF
create a cron job to run whenever you want to ftp the file
----------------
# minute
# hour
# day of month
# month of year
# day of week
# ---------------------
# run this cron every 30 minute, of every hour, every day, every
# month, daily
0,30 * * * * /FTPfiles.sh