How to make custom target board?

Creating a custom board is not that difficult. The QUARTUS II manual is very well detailed and if You follow all the steps, You will be able to get Your custom board created easily.

Being able to program the flash using the "Flash Programmer" is an other issue: You may end up to use the command line feature and not the NIOS IDE flash programmer unless You have one of the Flash Memories specified in the appendix of the Flash Programmer Manual.

One suggestion that I can give to You: create the custom board and include only the EPCS and any other Flash component; even if the feature of assigning the FPGA pins during this process, I found more convenient to do all the assignment in QUARTUS II. This approach will allow to reuse the same custom board configuration (FPGA + EPCS + Flash) over and over without the need to create a custom board for every single project. Moreover, this will allow You to modify the pin out of the FPGA even with the actual PCB already developed, without the need to go back into the custom board creation process again.

Have fun.