How can I direct run nios programmer on epcs?

You can't.

The EPCS ROM and sd card devices can only be read by device drivers (etc).

You could arrange to map multiple functions to the same addresses and load the code blocks are required (overlay loader) - but I'm not sure that has really been done since paged memory systems became common in the late 1970s.

Another option is to enable the mmu, take the page faults and use that to dynamically page in the required code - but that is a lot of coding, and I suspect you won't have enough real memory for a reasonable set of working pages.