We have shown that it is possible to input heat to one location of a molecule and simultaneously measure its arrival in real time at two other locations, using an ultrafast flash-thermal conductance technique. A femtosecond laser pulse heats an Au layer to similar to 800 degrees C, while vibrational sum-frequency generation spectroscopy (SFG) monitors heat flow into self-assembled monolayers (SAMs) of organic thiolates. Heat flow into the SAM creates thermally induced disorder, which decreases the coherent SFG signal from the CH-stretching transitions. Recent improvements in the technique are described, including the use of nonresonant background-suppressed SFG. The improved apparatus was characterized using alkanethiolate and benzenethiolate SAMs. In the asymmetric 2-methyl benzenethiolate SAM, SFG can simultaneously monitor CH-stretching transitions of both phenyl and methyl groups. The pheryl response to flash-heating occurs at least as fast as the 1 ps time for the Au surface to heat. The methyl response has a faster portion similar to the pheryl response and a slower portion characterized by an 8 ps time constant. The faster portions are attributed to disordering of the methyl-substituted phenyl rings due to thermal excitation of the Au-S adbonds. The slower portion, seen only in the methyl SFG signal, is attributed to heat flow from the metal surface into the phenyl rings and then to the methyl groups.