The windowed scale is for pure windowed mode, it will have no effect on full screen or windowed full screen mode, it only determines how big the window will be when it loads in a window.
My honest opinion for the best option for N64 emulation if you just want one emulator is to use the stand alone Mupen64plus, PJ64 is also ok. Unfortunately right now N64 emulation is kind of in a shitty state, it needs work.