for best results try setting them more like a arcade control panel, dont ever use your arrow key's for direction control (unless your left handed), try setting the control stick to: W=up, S=down, A=left, D=right, and use your number pad for setting the A,B, and C buttons (set the L,R,D and Z buttons were you see fit). thats the most basic and easiest layout to get used to.
tho using your keyboard gets tyring after long hours of zelda, and it dosent give you that kick back and relax console fell,
thats why i recomend one of these:
(this pad fells like it was made for n64)