Actually, the portion you read has nothing to do with nios2-flash-programmer, but rather the code that will be running from each processor.
Here's the key statement from your flash programmer dialog, that you missed:
--- Quote Start ---
Please use the configuration dialog to pick one, or specify the--device and/or --instance parameters on the command line.
--- Quote End ---
There should be someplace in the GUI that allows you to select a processor for flash programming. Alternately, you can modify the generated flash programming shell script (generated in the Debug/Release subdirectory of your project) to include an "--instance" option on the command line that calls "nios2-flash-programmer" and then run everything from a Nios II Command Shell rather than the provided GUI.
Cheers, and Good luck!
--slacker