Many CNC operators using a touch off plate are used to setting the origin Z0.0 to the top of the work piece, in their machining strategies.
RapidChange uses a fixed position tool setter when setting the tool offset each time it changes tools. It will reference to any value you choose for the SET TOOL OFFSET.
Since the bed of the table never changes this is the most reliable reference though it means that the origin Z0.0 will be the table bed.
If you are used to referencing with a touch off plate on the top of the material to be machined. Then you must change from setting your origin Z0.0 on top of your material to the bottom.