ported enclosure, sq

It's not unusual, when working with WinISD and following the Help files, to look to other sources for additional information.  See  http://www.lalena.com/audio/basic/terms/ .  For the info you cited re: "transfer function magnitude", look at this graph as a representation of relativity.  With the "0" red line being flat, responses below this line are lower in db while above the line higher. 

The relatation to SQ is in the peaks of the response and in the slope of the response's fall.  Some woofers will show a peak above the reference line and you will notice that the peaking diminishes as you provide more airspace.  At the same time, however, you will notice that cone excursion can quickly get out of control with the larger airspace.  You have to reach a compromise in freq response by checking all the available graphs when designing your enclosure.

For SQ you will try to reach as flat a response as you can...there are a lot of reasons.  The vehicle itself will cause peaking (cabin gain) and you don't want to add to that bandpass region unnecessarily.  +3 db shows an accoustical doubling of power to that frequency range.

The author's wording described "efficiency" and "n0" when describing this graph, but you shouldn't be concerned with driver efficiency while working with this program.  The efficiency is what it is for any given driver.  Use this graph to help you arrive at the best airspace to allow for maximum flat response while keeping cone excursion under Xmax at your specified power input.

Port tuning:  adds additional sound to the woofer by using a resonator.  You will see the results of the port by looking at the graph "Rear Port - Air Velocity".  It shows output of the port only and at what frequency.  You will notice that the resonance is at about 10 Hz higher than Fb (box tuning freq) in most cases.  For SQ I like to tune as low as possible.  Sometimes it is the case where port output is virtually nonexistant in a SQ vented box.  The venting is done because it is the best way to utilize the particular woofer...such as where using it in a sealed box limits, too much, the low end freq response.