Measure all wood pieces to be worked on and make sure they share the same thickness. You can do this by creating a set thickness prior to the start of construction. It is ideal to use only one piece of board to create all your rail and stile pieces so that they already have the same thickness.
Insert the rail router bit into a table router and set the bit height for the appropriate thickness of the wood panel you need. There should be sufficient material at the back part of the groove to ensure that the panel has enough support from behind. Make sure that the tongue of the bit is centered on the wood.
Cut the extra rail ends using the rail router bit, then make the necessary adjustments to the tongue's thickness with shims that may either be added or removed within your cutter. A shim is a washer or thin strip of metal used to align parts and make them fit better. Using shims is highly beneficial in adjusting the bits and setting up the blocks accordingly.
Use the stile bits to make the grooves in the wood panel. The depth of a stile bit must follow your planned measurement so that the groove gets the same height as the tenon, a projecting piece of wood inserted into a mortise of another piece. Take note that joints will get misaligned if the height is not set properly. Match the groove cutter to the tenon on the rail, then manually adjust the stile bit until you get the right measurement.
Make sure the rail cuts and the stile grooves interlock perfectly upon removal of the entire tenon with one pass from the stile bit. Reset the depth of the bit if you encounter any problem when removing the wood in one pass. Once successfully done, finish machining the pieces and expect the rails and stiles to fit accordingly.