The city plans are designed to allow you to have as much "hands off" an approach as you wish. So if you want to still control everything, you can, or you can let the settlers with their leader do all of it for you. You still have to do some stuff, but your involvement is intentionally minimized. I would stress, though, that moving the foundation and city skeleton objects around is not a good idea, as the city will upgrade to level 1, 2, and 3, building upon what is already there as part of the city plan (I know the level 0 skeleton is not that impressive, but wait until you see just level 1 Sanctuary.. it is a damn joy and looks like a real post-war settlement now). So, in general, not a good idea to go shuffling things around unless you'd like your upgraded city to resemble a Picasso.
The crafting benches got scrapped. They were in the way. You'll have to build new ones. If you don't have the perks necessary yet, an alternative is to move them to somewhere safe, like down by the river, until the city planning is done, then move them where you want.