Once you have your 3D terrain you can then use a tool called drape. This allows you to drape certain objects from the layers onto the 3D terrain. Select the layer you want to drape and select the terrain then click the drape tool.
Trees, using fully realistic 3D trees can look amazing but slow down the program a whole lot. However 2D trees may not show enough detail and won't look right from an overhead viewport. So you want a hybrid of these two. Basic 2D planes but several of them to make it look 3D.
Placement of trees should be easy now that you have draped on the tree's locations.
When draping items onto the terrain such as the road and boundary lines that you may want to texture you want to make sure that they are fully closed entities. So that when its draped it will remain closed, and so allows you to texture it.
Once tweaking the terrain a bit until it's satisfactory you can then create viewports for Layout. Change your viewpoint to have it completely flat. Next, go to the overhead view of your model and hold shift+z then hide all layers except the ones you wish to include in Layout. Add styles as needed and do this for each layer.