It is usually better to machine the heads rather than the intake. That way you can swap intake manifolds without having to machine each intake.

A good rule of thumb on a BB Mopar is to make sure that the intake side of the cylinder head meets the valley rail on the block and the deck surface of the block at a point. All three lines should meet at the same point.

Some machine shops forget to mill down the valley rails when they deck the block and then that causes all sorts of alignment issues during assembly. It is also a PIA to fix since the entire short block has to come back apart.