Hi:
Yes, you could make your nios-2 boot-up from the EPCS and also have aplication data there, IF your code and data are small enough to feet in the EPCS space not used for FPGA configuration data.
Using the flash drivers in the HAL your will be able of reading/writing from/to the EPCS. Determine a free location in EPCS, read the content of the entire block and reprogram with the content that must not be modified and the new data.
There has been a lot of discussion on the booting from EPCS subject on the general discussions forum, take a look at there.
Good luck!