You can try to create a batchfile (I guess you are on windows, because you use cygwin, on linux use a shell-script) that calls the commands you need and set it as "Output filename" in the projects "Properties -> Build targets -> [the target you use]".
That method doesn't seem to work. I have auto-generate file prefix and extension off, and I made a run.bat file to run the command and set that as the output file name. Clicking the run button does nothing. However, opening cmd and cd'ing to the directory which it is set to run in and calling it ("..\run.bat") launches it fine. Also, I don't need console output as I'm running it in qemu.
Configuration:
(http://dl.dropbox.com/u/11416717/config.png)
Run.bat:
C:\qemu\qemu.exe -m 32 -fda kernel.img -boot a
The run.bat file should work fine if it's actually getting run in the correct directory.
EDIT: By does nothing, I mean that qemu doesn't open and no output shows up in the console.