How to Synchronize Two Windows:
Open and process the two spectra.
Choose Window > Tile Vertically (or Tile Horizontally, or Do Not Tile, according to your tastes).
From the same menu, either choose Synchronize, if you have applied the same experiment to two different samples, or choose Smart Marks, if you have applied two different experiments to the same sample. There's an exception: Synchronize is the best choice to compare two homo-nuclear correlation experiments, for example a NOESY with the TOCSY of the same sample.
Synchronize: the navigation commands imparted to a window (zoom, cut, panning, etc...) are sent to the other window too. Marks and the Cross-Hair tool are duplicated as well.
Smart Marks: Only the marks are duplicated, and only when the observed nucleus is the same. If there is an homo-nuclear 2-D experiment, the horizontal marks are copied from the vertical marks.
To halt the mechanisms above, choose the same command again.