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.
Now you must define the extent of the extraction aperture. For boxcar extraction this is simply the width of the boxcar function. For optimal extraction we approximate the user-defined width as +/- 2 sigma for a Gaussian weighting function.
Press "A" or select "Apertures -> Define Center/Width" and the following dialog box should appear:
This box allows you to tweak the center location of the trace, and enter the extraction width by hand. The aperture center is defined as the fractional location from the left edge of the slit to the right edge, with 0 being the left slit boundary and 1 being the right boundary. The reason for this is that FIRE's prisms introduce optical distortions that make the plate scale non-uniform across the detector, but the fractional position is preserved.
The aperture radius is defined in pixels for software compatibility reasons. This could be changed to match the fractional positions if there is an outcry from the user community.
When you enter in the desired values and click OK, the aperture boundaries are added to the GUI as dotted lines. 
You may return to the aperture dialog box to readjust your values if you wish. When you are happy, click "done" or type "q" to exit the aperture definition GUI and return to the pipeline. Another xatv GUI may pop up immediately after to confirm your object placement; you can ignore this instance and quit out to proceed with the object extraction.