Rich…
To address your questions, the PM42 has (4) outputs where each can be configured (jumpers) for short protection OR auto reverse but not both for any given section output.
I configured my 15’ x 16’ layout in (3) electrically isolated short protected sections using (3) of the (4) PM42 outputs, with (2) of the protected sections ending in return loops but connected by a long run between them with the center point as the end of protected section (1) and the start of protected section (2).
The third section of my layout is a 36 foot long out and back design that begins and ends off of the larger of the two return loops (section 1) and why I chose to electrically isolate it for circuit protection with a 3rd PM42 output.
Just to add, Digitrax recommends using a separate AR1 (or multiples) downstream from a PM42 output to provide short protection for trackage inside AR1 powered return loops.
To give you a better visual idea this is a link to a February 2012 forum post with some pics of my layout at the time including my drawing (since slightly modified but essentially the same overall). Kinda’ messy but at this point I was in full roadbed and track laying mode with all the requisite crap scattered atop the benchwork…(smile)…