I don't have Empower 3, so if this functionality is very different from Empower 2, this answer won't be very helpful - sorry about that.
The attached file describes how to do this subraction in Empower 2 with some screen shots. I put this together for an unusual application where you were subtracting the standard from teh sample to look for differences....
Hopefully this can get you going.
There is no difference in the procedure on how to do a blank/baseline subtraction in Empower2 and 3 so you can use Kevin´s procedure. The "blank" column you are referring to is used for signal to noise calculations where you can use the noise from the injection labelled "blank".