You need to edit struct epcs_partitions[] in file linux-2.6.x/drivers/mtd/maps/epcs_map.c .
It divides the epcs to partitions, eg, fpga config, (+) kernel image, jffs2 etc.
The epcs partitions will become device /dev/mtdblock0, /dev/mtdblock1 ...
Then you can access each partition just like a regular file, or actually block device, with file operations such as open(),lseek(),read(),write() and close().
Update the firmware means, write the file.
Please read the wiki pages for details. It will be more clear when you walk through.