How do I store values in EPCS?

I think, you answered part of the question yourself. If not needing NIOS II for other purposes, you won't utilize it for EPCS access only. The SFL interface is present, if indirect JTAG programming is part of your design, otherwise yous can connect the EPCS pins as user I/Os directly. Finally a serial flash controller has to be designed. AN379 is one possible solution, but I don't know, if the reference design files are available somewhere, they seem to have vanished from Altera.com. Otherwise you can build it from the scratch, the programming algorithms are well documented in the Altera datasheets and also with compatible chips, e.g. M25P16.