By selecting "Interactive / User Defined" on the Object Finding section of the Extraction preferences, you will be presented with a GUI to aid in setting extraction apertures as the pipeline runs.
For each exposure, FIREHOSE first performs a crude first-pass sky subtraction to assist in locating the object in the 2D frame. A display GUI will pop up showing the sky-subtracted frame. Below I show an example of this GUI for an object showing a single emission line near the center of the display but no continuum. 
A summary of key commands may be obtained using the Help -> Aperture Def Help menu on the menubar.
To define the trace location using the GUI, center the cursor over the emission line (or any location on the image) and press the space bar. A cross will appear to indicate the location of your choice. You may define many crosses and the software will use the median spatial location for the aperture.
If you are not happy with your location, press "C" to clear and start over. However if you are happy, press "O" to extend your trace location to all wavelengths/slits. FIREHOSE uses the map of the order boundaries to define the shape of the trace. A black line indicates where the center of the trace has been defined, as shown below.