using NIOS II Stratix II (EP2S60) board as FPGA

Hi! Sorry, I'm new here.

Got this board: Nios II Stratix II (EP2S60) ROHS.

Now, with all my respect to Nios ideas, I willing to use EP2S60 chip just for my another design, not related to Nios.

My question is how correctly to reprogram MAX7000 loader to do so EP2S60 will always boot from EPCS64? I cannot boot from flash memory, becase I'll need to use it with different reason. I tried to set MSEL lines as 1001 but I'm not sure it's correct. Should I also check another EP2S60 configurating lines?

Also, my question is, how to program EPCS64 memory correctly? Quartus Programmer sometimes working, sometimes not... probably depending on chaotic things I do with the board. So that is why I need advice.