programming configuration flash with some data

Have a look at the "altera serial flash loader ip core (http://www.altera.com/literature/an/an370.pdf)". This gives you access, from the FPGA fabric, to the pins on the serial FLASH. This would allow you to read from (and write to) the serial FLASH from your own logic.

If you need something a little higher level then you could consider Altera's "avalon-st serial peripheral interface core (https://www.altera.com/ja_jp/pdfs/literature/hb/nios2/qts_qii55009.pdf)". This implements the low level serial comms to the serial FLASH device offering you a simple Avalon interface to your own logic. You might also want to refer to the "spi slave/jtag to avalon master bridge cores (https://www.altera.com.cn/zh_cn/pdfs/literature/hb/nios2/qts_qii55011.pdf)" for some more info on controlling this.

Cheers,

Alex