First off, I want to be sure I fully understand your situation. Looking at the kits decals and the picture from the instruction sheet it would look as if they don't provide a decal to fully cover the black portion of the hood. I would suggest painting the portion of the small portion of the hood that needs to be black and isn't covered by a decal after the body color is applied. After the paint has dried then apply the kits decals. Then you would clear everything. Now one problem that may or may not be an issue would be if you want a gloss finish on the black areas or a flat or semi-gloss. This is where the masking you mentioned can get very tricky. Just about any masking tape going over a decaled area has a very high probability of lifting the decal when the masking tape is removed. I would just paint the hood, apply the decals and clear everything. Going for a flat or semi-gloss black finish you would mask off everything but the portion of the body you want painted black. How comfortable are you with masking the black pattern would be the big issue.