Subtracting B from A to get: C = A - B
Bring document A to the fore. Expand the region(s) with the most important peaks; in this way you can monitor what's happening.
Choose Format > Overlay.
You will see the list of the other windows. Check the box at the left of the name of B. Now the spectrum B is drawn over A.
Set the pre-multiplication factor for B (it's reported into the last column, “amplif.”). Set a positive factor for subtraction and a negative factor for addition. You can type the value or modify it with the little arrows at the bottom of the same column.
Click Apply or press Return to update the plot.
Click Subtract: you'll see the difference A - B instead of A.
B is still on display. You can still change the pre-multiplication factor, if you need. The subtraction too is reversible.
When the result satisfies you, close the dialog. B disappears and only the difference spectrum remains.
It's not enough to save A, because iNMR never overwrites the original spectrum. If you want to store the difference, choose File > Export and create a new iNMR document.