After setting up the preliminaries, the subsequent steps follow in order of the buttons on the GUI from top to bottom.
First up is tracing order boundaries. Press "Trace Slits" to run.
The code will take ~10 seconds to do this and present the user with an atv window to confirm that one slit (indicated with '1's on the display) has been found. The "red" flat is used for this calculation, since saturation causes problems in the tracing (and the red flat will be unsaturated). If saturation is present in your flat the tracing may fail altogether, in this case try using a science exposure or other unsaturated frame.
This procedure creates a file in the "Flats" subdirectory of the reductions master folder called Slit_xxxx.fits. The first extension contains the binary 1/0 slit mask, and subsequent extensions hold IDL structures specifying coefficients of the fits.