several questions about making my target board

I misunderstand you. Do you means : is it necessary to add new Nios when you create new nios system after creating "target board"?

Yes, obviously, you should add new Nios and Jtag, and some other components to implement what your thinking. The "new system " project and "target board" project" are in diffrent usage. The "target board" project only using when you use "Flash programming" to programming "new system" project ( the "target board" project will programming to FPGA first to programming "new system" project to Flash, then after power reset, the "new system" project will work.)