Hello
The model need to be included in the file that represent your NIOS (at the bottom of the file).
You will find locations where you can include your code :
-- <Altera_Note>.....
The code will not be removed when you re generate your NIOS II system.
This is the idea.
To check my design , I had no time to perform what is described above, but this is the philosophy. Instead , I have used the internal memory under Modelsim , and use SDRAM in the real product.
This was to be able to check a full design (NIOS + Logic) together.
Also , you will have to set the NIOS II software/BSP (under Eclipse) to generate the correct file for SDRAM or Internal Mem.
Ben