There are two methods of programming using the Quartus II Programmer.

1: Populate J16 with header pins, set the Quartus II Programmer mode to "Active Serial Programming",
Write pof file.

2: From the J4 USB port, set the Quartus II Programmer mode to "JTAG" and write the jic file.
The procedure for doing so is shown below.
・ Use Convert Programming files function from sof to create jic file
・ Start the Quartus II Programmer and register the jic file
・ Press the PGM_SEL (S7) button on the kit twice to light the EPCS LED
・ Click the start button in the Quartus II Programmer to execute programming
・ After completing the program, turn the power OFF ⇒ ON.
・ Press PGM_LOAD (S8) to execute configuration from EPCS

Regarding the writing method,
<install directory>\cycloneIVGX_4cgx150_fpga\documents\rm_civgx_fpga_dev_board.pdf
Please refer to P2-15 of
Note that switching between AS mode and FPP mode is controlled by the MAX II device, so if you want to check the internal circuitry of MAX II,
<install directory>\cycloneIVGX_4cgx150_fpga\examples\max2\max2_c4gx.qar
Please refer to