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I'm not sure if you can do this in the BSP Editor, but you can try.
You can check if it shows in the Linker tab the Flash Memory, if it's there you can have access to this part of the memory creating a variable/vector in this section (using .xxxx). It will probably work this way, but it'll be slow.
I think the best way if you're going to use a NIOS processor is to transfer data from the FLASH memory to the SDRAM or Onchip Memory.
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Would be glad if you can send me a NIOS project example as i haven't worked with NIOS before. Thank you