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.