Use the EPCS controller and set your reset address to that device. The EPCS controller includes a bootloader that will copy the software out of the EPCS device.
Then in the IDE you use the flash programmer to populate the hardware and software in the EPCS device. I assume you have a target configuration already that you have created for your board already. You can do this from the command line too but I would give the IDE a shot first. So the 3 steps you describbed are possible (well except 2 is contained in the EPCS controller). Check out the EPCS controller document up on the Altera site for more info.