The exposure mode does not make any difference. Only the actual exposure. But switching to manual and setting the exposure settings from your ground spot metering is a good start.
On the other hand, from your description, it's hard to believe you got a blown out sky, unless your ND grad was upside-down. Was the darker part of your filter on the top or bottom?
Adding he ND as you did, setting exposure compensation to 0, and setting ANY exposure mode aside from M should yield a decent exposure unless something is wrong. Setting the camera to manual and then adjusting until the meter says 0, would effectively do the same thing.
In any case, i think you ND grad was upside-down, or something else was dramatically wrong.