You should upgrade to V3.52 for major enhancements. You could “Save Ref” to save the reference signal (in this case “Freq Out”) first. Then “Load Ref”, connect probe to desired signal and then use “Show Ref” and “Hide Ref” to compare the two signals… You may want to refer to the training videos at:
youtube.com/user/lwgraves?feature=mhsn#p/p
for additional information.