I was watching a gardening program yesterday and they suggested putting a layer of cardboard or 5 to 6 layers of dampened newspaper over the clumps.* The cardboard/paper would break down over time and the lack of sun to that part of the soil would smother the wild onions and wild garlic.* I would suggest you pull back some of the new topsoil and put down the cardboard or paper and then cover that with the newer soil.
To tell which you have, wild onion leaves are flat and wild garlic's are tubular.* Both are edible if you haven't sprayed with toxic chemicals but the wild garlic is much stronger then most garlic you purchase in the grocery or grow in your garden.* The odor persists much longer on the breath with the wild variety.
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.