Question: are you using any pipeline bridges?
You should create the qsys component at the end of the design and add your files at the same time. Add the simulation files as well so you can create a testbench of the system. I usually dont change the default Explicit Address Span and usually works fine. What i do see what is important is having the correct timing diagram for each signal. I have ran into a lot of timing problems because i have overlooked them. The test bench will show you some of these issues. Also you can add a nios system into the design if your having problems seeing the address. When you create a nios system in eclipse the system.h has the addresses stored. you can use nios for testing as well. Hope it helps :)
-Trukng