1. You can make underground maps by going into mapmaker and unchecking the 'sky' box. To make tunnels on an open sky map, you'll need to use some combination of meshes and ravines; the heightmap doesn't allow for actual tunnels.
2. Most people make meshes in Blender, which is a free 3D modeling software. You'll need to either learn to convert them to a format that FeralHeart can read, or find someone else who can in the forums.
3. It is; you can adjust the size in Mapmaker.
Hope that answers your questions!