Hi Molder,
What format is your data in? If it's two waveforms, two arrays of doubles or even two dynamic data type that are generated by an express VI, you can actually subtract one set of data from the other to find the amplitude difference. The subtraction vi should be under Numeric->Subtract. If they are two waveforms and there's a phase shift between the two, you have to make sure to account for the phase shift. If they have different frequency, you'll also have to account for that. Basically when you do subtractions between waveforms, it subtract the value amplitutes at the time when data is acquired based on the time stamp on the waveform.
Hope this information helps.
Yi Y.
Applications Engineer
http://www.ni.com/support