I use AIP4WIN for aperture photometry. My pragmatic approach in trying to measuring SNe is to choose an aperture for the SN itself which extends out to where the SN light distribution blends into the background but no further. Then a small gap of a couple of pixels followed by an annulus which includes at least 10 times as many pixels as contained in the central aperture. This will inevitably include light from the surrounding galaxy but the distribution of this light is likely to be a gradual slope as you move away from the galaxy core. The annulus will record an average of this background intensity which should be reasonably representative of the galaxy background under the SN itself. You can try varying the various radii involved to see how stable the result is. As I say this is a pragmatic solution and not perfect but in my experience it seems to give a result consistent with other reports.
David