Your circuit obviously has two loops, one from the output to the input of the first stage, and another one from the output to the input of the second stage. You must put the probe into a wire that breaks both loops when opened, so the position in your schematic is correct. For details, see the section "Applicability of Loop-Based and Device-Based Algorithms" of
http://www.kenkundert.com/docs/cd2001-01.pdf, this is the article that describes the algorithm used by the stb analysis.
For a circuit with negative feedback, the phase of the loop gain is supposed to be -180 degrees at low frequencies in stb analysis. For details, see
http://www.designers-guide.org/Forum/YaBB.pl?num=1124688329.