StratixIII kit: store FPGA config + NIOS.elf using the NIOS-IDE flash programmer tool

Dear Madam/Sir,

I have designed boards based on CycloneII FPGAs for which, having implemented a NIOS-II in the FPGA, I found very convenient to store FPGA .sof configuration file + NIOS hex code into the serial conf device (EPCS64) using the NIOS-IDE flash programmer.

I have purchased a stratix III dev board on which a MAXII device is instead acting as a configuration controller and I am disappointed at seeing that what was so straightforward before it is now so obscure.

I have been struggling quite some time but

I couldn't find a clear explanation about storing the .sof and the .hex in the flash so that the MAX-II could fetch the proper information from it; having the code for the MAX-II could help some. Could You please tell me how to use the NIOS-IDE flash programmer to store both configuration, NIOS executable and the bootloader in the flash device?

Why does ALTERA put a black box such as the configuration controller on a development kit which should serve as a tool to learn new tecniques?