DE1-SOC 5CSEMA5F31C6 can't be detected

First, I am glad to see that you are able to detect the 5CSEMA5F31C6 device using the programmer now. So that's one problem solved.

Secondly - I think you might've been confused with what the sof file does, and how to use it. I suggest going through Terasic's my first FPGA tutorial; in the meantime I will try to explain here (but trust me, it is easier to understand if you follow the guide hands on)

A sof file is a programming file that is generated each time you successfully perform full compilation of your design in Quartus. For example, let's say you implement a blinking LED using verilog code. Once you compile it, a sof file will be generated (it is usually located in the output_folder directory of your project location). Then, using the programmer, select the FPGA (put a tick box on it) and download the sof to the FPGA. Then, if everything goes well, you will see the blinking LEDs on your board.

You do not have to use the University program's DE1_SoC_computer.sof if you are writing your own verilog/hardware design in Quartus. The aforementioned sof file is provided for users who are interested to debug/learn about the software implementation in DE1-SoC. In that way, they do not have to design the system from scratch.