I don't use the IDE at all.
Since I'm downloading using PCIe (we've exposed the nios soft-reset to the PCIe slave<->avalon bridge) I don't have any altera software installed at all.
I use a copy of gcc (+binutils) built from the sourceson the altera ftp site and my own makefiles.
The binary code+data for the nios is actually linked as binary data into a ppc linux program - this requires a system with both cross compilers installed!
You do need to think of how you are going to get the code/data loaded in the field. Especially if you might want to do field upgrades. Anything of that nature is likely to be more friendly during development than having to rebuild the sopc image or download the code using jtag. Also best tested early!