NIOS II and ASMI

To answer your original question, the only big differences between the EPCS and ASMI cores are the inclusion of boot support and the HAL software interface.

If you are using the altera_avalon_epcs_controller peripheral you can simply read and write the EPCS device using the HAL flash API. For example using alt_flash_open_dev(), alt_read_flash(), and alt_write_flash(). Details are given in chapter 4 of the Software Developers Handbook.

Nothing is particularly "secret" here. All of the source code has been made available, so that if the published interface doesn't meet your needs, it's easy for you to change the code.

However sticking to the higher level published API is recommended simply to save you time. It will save you time in the short term, since you won't have to reinvent the wheel, and it will save you time in the long run since it's that interface that Altera wil try hardest to maintain in future versions of the kit.

In this particular case it also means that you will be able to use the same application code to read/write bulk data regardless of whether you store it in an EPCS or CFI flash device, or future devices that will be supplied with HAL flash drivers.