in windows, go to the directory where the files you want to transfter to the board and then type command: ftp "board ip address". In windows ftp command enviroment, go to the mounted compact flash partitions(be aware that you may need to change the mode of the partition to writable) and then type: put "the file name in the windows directory"(be careful that you need to set the file type before transfer under ftp command, such as command binary and accII etc. Use help to view the command functionality).
The files can be easily transferred to compact flash.