As you saw before when I was removing baselines, you can subtract the X register from the Y register and have the difference become the new X register. The command is subtract-spectrum. SPECX can also add the X and Y together and average them. The commands are add-spectrum and average-spectrum. average-spectrum (ave is enough) is the usual choice, and uses weights when averaging that are determined by the integration time divided by the square root of the system temperatures of the two spectra.
While I'm on the subject, SPECX also has multiply-spectrum and divide-spectrum. Skipping the conversational mode the commands would be e.g.:
mult 2.0
and
div 7.8
The defaults factors are set to unity (they used to be zero).
Specx Cookbook