Need some help of SRunner Tools! Need some related files!

What do you mean by editing .rpd files? The file format is proprietary to Altera, so you do not get to edit anything. You can use Quartus to generate .rpd files, and you can use SRunner to download them.

The S in SRunner stands for Serial, since the EPCS and EPCQ are really just re-branded SPI flash devices. You can read any number of SPI flash data sheets to understand the op-code and addressing schemes used by these dvices, eg., Micron data sheets are good.

What you do not get to "learn" is what is the format of the .rpd file, eg., how do the bits in the file correspond to programming cells in the FPGA. That is the information Altera does not release.

Note: because you mentioned .rpd files, you implied you are interested in using an SPI flash for FPGA configuration. If the SPI flash is larger than the configuration file size (compressed or not), you can use the remaining flash, eg., to store NIOS processor code, or user-defined data. After the FPGA configures from the SPI flash, the SPI interface pins can be configured as user I/O and you can use an SPI master in the FPGA fabric to access the flash.

Cheers,

Dave