"On their website when booking a flight under stops it usually has the airport listed...."
If there is an airport listed, it's a connection city.
"When it just says (2) does that mean 2 stops? "
The number is your total number of stops enroute on a direct flight, or total number of stops including any connections with direct flights.
As far as BNA to SJC, the routing is flight #160 leaving BNA at 1:50pm. This flight stops at PHX before going to SAN, where you connect to flight #571, a nonstop from SAN to SJC arriving at 7:30pm . The total stops enroute is 2. This is coded as SAN/2.
The timetable & website don't show the aircraft used, but a quick call to 1-800-I-fly-SWA will anwser that question.