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 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.