Don't want it to Round up??

There is no need to use two variables for same field.

toFixed() will still round result.

You can use this:

var v1 = Number(this.getField("NMS").valueAsString); 
var v2 = Number(this.getField("CMS").valueAsString); 

function twodecimals(v, d) {
return (Math.floor(v * Math.pow(10, d)) / Math.pow(10, d)).toFixed(d);}

if (v1==0 || v2==0) event.value = ""; 
else
event.value = twodecimals((v1-v2)/v2, 2);

Set the field's Format to None, and change the end of the code to this:

if (v1==0 || v2==0 || v3==0) event.value = ""; 
else event.value = ((v1-v2)/v3).toFixed(2);