1) depending on address
when you see addresses on SOPC builder (or Qsys) the address itself is the way to access each IP.
this function gives value 0xff to address 0x00100 (+ offset 0 ).
IOWR_32DIRECT(0x0000100, 0, 0xFF );
2) sorry.
I have no idea.
3) you can not run c code on NiosII.
C program runs on your CPU. and CPU analyzes your code each time.
you can never run C-code (even assembly language) along with each clock.
that's why you need to create custum-IP core.
4)maximum PLL clk.
sorry I don't have much time to reserch.
I always use 100MHz for CPU clock.
coz, that is enough. even if you want to use 1GB/sec stream.
on your case. you want to create custom IP-core such as HDL-core which you can command from NiosII( avalonMM master).
there is easy-text I wrote long time ago.
http://www.akiron.com/fpga/customipinstruction.pdf see you.