using extra space in serial rom

You can try to use the ASMI (altasmi_parallel) megafunction instantiation to access the general purpose memory portion of the serial configuration device, EPCS through Cyclone III device. You can store the configuration data in .rpd format into the EPCS. The altasmi_parallel megafunction provides access to the memory of an EPCS device through parallel data input and output ports. The .rpd file is a binary file for EPCS devices containing a binary bitstream of configuration data for FPGAs that support Active Serial configuration.

You cannot write/store the other data starting address 0 because by default it is the memory location for storing configuration data. You need to make sure the data you intend to store does not overlap with the configuration data. Check the end address for configuration data in the map file, then you can store data into other memory location.