I won't be of much help here, as I don't build SOPC/Nios systems, so maybe someone else can jump in. Note that the SOPC builder has a common flash interface controller:
http://www.altera.com/literature/quartus2/lit-qts-peripherals.jsp And you might want to explain in more detail what you've done, as I'm not quite following. For example, you have a top-level system that is, or instantiates, an SOPC system with Nios. Are you then adding a flash controller and it's failing, or do you have source for a controller and are trying to make a peripheral? Etc.
(Also, another resource to look at is niosforum.com.)