Flash Programmer--MMU

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Do I also have to add these offsets in custom_fpga.h or is it only necessary in these commands?

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Don't modify custom_fpga.h, just use the correct addresses in the commands. Drivers will use the addresses in custom_fpga.h and ioremap() them as appropriate.

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Do I have to add this offset( 0xc0000000) in the command sof2flash for the EPCS?

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I don't know much about programming EPCS, but this is what I do to program in the FPGA configuration image:

sof2flash --activeparallel --offset=0x20000 --input=/data/nios/myfpga.sof --output=myfpga.flash
nios2-flash-programmer --base=0xe4000000 myfpga.flash --instance 1

My guess is for EPCS you just replace --activeparallel with --epcs

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I don't know where to add --mmu option, could it be this place?

nios2-flash-programmer --mmu --base=0x08800000 ext_flash.flash

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That looks right.