S21 is the ratio of voltage at port1 and port2 so yes you need two ports. I can tell you right now doing this right: " I have basic micro strip shape and I need to measure permitivity and permeability of the shape.." this is a tall order if this is just something for a class project that's one thing, but if your doing this for real you are going on a year long adventure. You will be up to your ears in surface roughness, causality, passivity, dielectric and PCB construction, solder mask, etch angle,etc. Why are you doing this ? it's likely over kill for your project. bellow 20ghz just ask your PCB vender to make a 50Ohm micro strip and you should get 50+/-10 Ohms ( +/-5 if you pay extra).