Open the group that the "hole" is in and pick the edges of the hole, then from sandbox tools select from contours. It should generate the "triangles" as needed to fill in the hole.

I don't know about a plugin but i think you can just double click the face inside to select related geometry and Ctrl+Move upwards to make a copy, then make it group and move downwards. Then you can hide/unhide the group as you wish. (Also you can delete the geometry (edges created) on terrain mesh)

As Pilou points out you need to split the wall up to paint different faces.

Afterwards you can use Combine Textures to merge different materials into one material.

It's clear from the various posts that you have many options when adding a roof over these walls.
The last poster's suggestion is to ignore the masonry walls and make an orthogonal roof over them with parallel eaves and ridges, but with varying soffit dimensions.
If this is acceptable to you then you might have as a simple roof structure and finish as you could.

Otherwise if you must have parallel eaves and ridges you must either accept a roof surface that is not in one simple plane, with twisted facets are needed to achieve the form, or a piece of 'flat' roof at the ridge to fill in the inevitable gap between the two single-plane roofs that meet there.
In these cases you need to consider the complexity of making the non-conventional roof structure and its finishes.

If parallel eaves and ridges are not a must, but single plane roof for each section are still preferable, then you need to decide it you are to slope the various ridges or the various eaves. The former is probably the more conventional structurally - it's effectively a very shallow hip construction with the normally horizontal ridge-board becoming in effect a sloping hip-tree - the roofing material is easily trimmed and covered by the ridge capping: otherwise sloping the eaves means non-conventional sloping wall-plates, odd-walling etc, and probably ugly weirdness at the lower edges of the roof, where material at the eaves would need cutting and finishing oddly - somewhat like a shallow valley gutter...

For trees , grass & flowers you have this free one! 😉
(Press "Download" button )

flower1.jpg

By TreeMaker

http://www.3darcstudio.com/images/master/verdure09.jpg

There is also Drop Vertices by TIG 😉

You're right. You have coincident faces. You could make the openings for the windows larger. They'd have to be in reality anyway so there'd be room for the window frames. You could also select those faces and create a group whose visibility can be turned off so you don't see them. Or you could simply delete the faces in the openings in the wall. If you're only going to show it with the windows in place, you don't need those faces anyway.

The best thing to do for hiding and showing entities between scenes is to group those entities and assign the groups to layers which can be turned on and off as needed for each scene. Leave all edges and faces on Layer 0 and just associate the groups or components with other layers. Although you could use Hide, managing it is complicated and can cause you more problems than it solves.

A 'container' is a group or a component-definition [it's also an image BUT that is not relevant here].
The 'container' contains a separate entities 'context', compared to the model's entities context.
So putting geometry into a 'container' separates it from its original context's geometry.
A 'container' can also include other 'containers - aka 'nested' groups or components.

Note that groups, component-definitions and even images are all 'definitions' as far as SketchUp is concerned.
All such 'containers' can be assigned to layers to control their visibility...

Images are a special case - a single face with a 'hidden' textured-material.
Don't fret about those at the moment.

A group is a unique collection of objects, copy it and edit the copy and it's not linked to the original at all.
If you delete a group then it's gone.
However, it's a useful way of separating/collecting objects.

A component-definition is displayed in the model as component-instances - it is a collection of objects - copy it or place another instance and they are all related.
Edit one instance and all other instances change to match.
This is a powerful tool.
However, if you want to split-off an instance the make_unique tool does that...