Thank you for your post.
If the waveform that you need to compare against is a stopped file, then yes this is possible.
Open two scope windows with exactly the same settings (if they are different this will not work). Then on one window select "Freeze/Thaw One" to stop the trace. Then go to View Composite and the two traces will be shown on the same axes thus meaning that the second window can be compared against the stopped window.
If you wish to do this with 2 live traces then you can either use channel A and B concurrently in one window, or the above method.