i like to set the reference at the z home position (this works well as long as your machine is homing to the same position day in and day out) and then you don't actually have to have a physical reference tool. and then after reference is set at home. measure tool height off a 123 block sitting on the table. (a fixed distance) . one con of this method is that the tool height offsets are big numbers -18" etc.. since the offset # is the distance from home to the top of the 123 block for that particular tool. or you could go with the standard reference tool method which is explained in this video starting at about 18 minutes into it.