All hardware in any Nios II based system can be accessed via simple memory reads/writes.
So, for example, if your hardware has registers at 0x00920830, then you can read from the first 4 bytes of your register by using something as simple as:
int *addr = 0x80920830;
int reg = *addr;
Notice that I turned on the high bit for the address of the registers. This bypasses the data cache so that I'm guaranteed to receive current data. Writing is done in the same fashion.
Since access is so simple, there are no macro's to read and write from hardware for Linux as far as I know.