Truth be told I haven't used the regular NIOS IDE since 7.1. I was not aware of any place where you could enter post-build commands.
Here is what I do remember doing. You have to add an external tool run configuration:
1 - Run->External Tools...->External Tool Configurations.
2 - Create a new program run configuration that performs whatever it is you're trying to do. You can use workspace and project variables. Under the "Build Options" tab make sure you correctly set the program up to run when you want it to (During manual builds, auto builds, cleans, etc.).
3 - Now for the software project you want to run the program for. Right click on the project and click "Properties". Once the Properties dialog opens click on the "Builders" section on the left-hand side. Now click the "Import" button. Then select the run configuration for the program that you created in step 2. Make sure it's the last in the list of builders.
Now when your build completes, that program should run automatically.
Or you could upgrade to 9.1 and start using the new tool flow which in my opinion is much better.
Jake