Does the Crop Map have to match the layout of my Farm Map?

No, and that is the point. On the Crop Map, arrange your blocks the way you plan them, whatever their place on the aerial view: the greenhouse next to the tunnels, the blocks you plant together side by side.

Your growing space on the Dashboard counts every block of the season, placed or not.

Beds, dimensions and tunnels still come from the Farm Map: to change them, edit the block there.

The steps are in Place your blocks on the Crop Map.