There are several large and complex formations providing some good overviews on what goes where, and the general structure of things as a whole. This is a very important page because it starts giving you a better mental picture of the ship to work with.
We need to look at two formations which were both found on the 12th of June 1999.
I can easily identify the following components as they relate to our model of the crop circle ship:
We have in this crop circle above, the microwaves passing through 9 objects. This means that microwaves are passing through all nine spheres of the large tetrahedron structure.
I am calling this Sphere Z (SZ), because it is the last major connection on the ends of the large tetrahedron structure, and it is different to the other 9 primary spheres on the large tetrahedron structure.
Interesting related formation:

Sphere Z appears to be a somewhat mysterious object at the moment. On the very same day as the 'Serpent' formation which we covered first, the next one, 1024 feet long, was also found. I have included the full image so you can see how detailed it is and how much information it can connect for us.
First and foremost, we have a sphere set which stands out clearly:
What we have here is a complex part of the ship at the bottom of the large tetrahedron structure. I can't say I understand it all, but I can say how it fits together.
Remember that what goes for one sphere set goes for all three, meaning that below, the three spheres in the crop circle represent all 3 sets of 3 spheres in the large tetrahedron structure.
Because a sphere set in a crop circle represents all three sets in the tetrahedron structure, it makes sense that there are also three of all the other objects involved in the area.
For example, we can divide the formation into something like this, and see obvious similarities in the objects involved:
These are all representing different aspects of what are essentially the same complex components.
Next, I have marked objects with numbers either 1, 2, or 3, depending on their position.
Now:
The object marked 3 in actuality is the watersphere, and therefore goes at the center of the large tetrahedron structure as we have seen. That means that objects 1 and 2 extend outwards in 3 directions from the watersphere, to the corners of the craft. There must be three of all objects which are not in the center of the large tetrahedron structure.
A few weeks later, we have a confirmation to make things clearer. You can compare the numbers with those above, to see how there are three instances of all objects that aren't considered in the center. Additionally, in the formation above, in a couple of the parts marked '1', there are hemispheres, as there are below where it has been marked '1'.

(COMPARE!)

We can being to see where everything fits... let's look at something else.
We have here something which is easy to miss. Look at the object in the black square below.

Does it remind you of anything?
Water!
On one of the first pages, we were able to identify these depictions of water:

So we can see that:
Furthermore, about a month after the formation marked A above was created, we get the following design:

We can see the connection here, with the watersphere being at the center of both formations.
Above, formation B appears as though something has 'exploded'!
Given that the power system of the crop circle ship relies on using water over and over again, as well as seperating parts of it into hydrogen at times, there would be a point where oxygen and hydrogen need to be recombined into water.
Could this explosion be the recombination of these elements into water, while providing some kind of pressure power to the crop circle ship as they do? Notice that the explosion goes 6 ways, not just 3.