Conclusion:
In the case of the atom, you wouldn't see anything without special instruments. This is because the object is so small that very few atoms will interact with it, so it imparts almost no energy to any matter that it encounters.
In the case of the marble, there would be a bright flash streaking through the sky, comparable to a large meteor, but much faster. Upon impact, the top layers of soil would be vaporized, resulting in a blast comparable in intensity to a very large conventional explosion (tens of tons of TNT). This would coincide with a small localized earthquake and a ground shockwave comparable to an underground explosion, due to the object passing through the rock at greater depths.
At the exit site, almost identical effects would occur, except there would be a large explosion followed by a flash streaking upward into the sky.
The exit event would happen $34$ seconds after the original impact, assuming the object comes down vertically and is moving at $370 \text{km} / \text{s}$ (see below about these assumptions).
Detailed explanation and calculations:
I. Hydrogen Atom
Let's first do a quick back-of-the-envelope estimate for how much energy would be imparted to the atmosphere.
- Object's speed relative to the Earth.
First of all, what does "at rest" mean? Let's suppose the object is at rest with respect to the cosmic microwave background (CMB). The rationale is that if it originated in the primordial Universe, then it would have originally been at rest with respect to the CMB, and if it has infinite inertia, then nothing can change its motion, so it will remain at rest with respect to the CMB. The Earth moves at about $370 \text{km} / \text{s}$ with respect to the CMB, so that's how fast the object would hit.
- Interaction with the atmosphere.
When the object passes through the atmosphere, then any atoms it comes into contact with will bounce off at approximately this speed, on average. Let's first calculate how much mass of air it will encounter. A column of Earth's atmosphere (from the surface to space) has a mass of about $10\mathpunct{,}000$ kilograms per square meter of surface. The object is about the size of a hydrogen atom, with a radius of $10^{-10}$ meters, so if it's a sphere, it will take out a cylinder of atmosphere with an area of $\pi R^2 \approx 3\mathrm{x}10^{-20} \text{m}^2$. Multiplying this by $10\mathpunct{,}000$ kilograms gives us $3\mathrm{x}10^{-16} \text{kg}$ of air that directly interacts with the object.
After this object passes, these air molecules will be moving around at about $370 \text{km} / \text{s}$. Using the expression $E = \frac{MV^2}{2}$ for kinetic energy, we get $$E = \frac{(10^{-16} \text{kg})(370\mathpunct{,}000 \text{m} / \text{s})^2}{2} \approx 7 \mathrm{x}10^{-6} \text{J}$$ energy imparted, in Joules. This is an absolutely minuscule amount of energy; for comparison, a normal household 10W halogen bulb emits 10 Joules of light per second.
- Effects on rock would also be negligible, so there is no need to calculate them.
The amount of energy deposited when the object strikes the surface will be similarly negligible.
In the above calculation, the energy imparted to an object is proportional to its column mass (mass per surface area).
Consider the first three meters of soil that the object passes. A layer of rock 3 meters deep has about the same column mass as the atmosphere. Therefore, the object would also deposit about $7 \mathrm{x}10^{-6} \text{J}$ in the first three meters of rock that it penetrates. Again, this is practically undetectable. It will, of course, continue depositing these tiny amounts of energy as it passes through the Earth.
II. Marble
In the case of the marble, the calculation is almost the same as above, except the object's radius is now more like $0.01$ meters instead of $10^{-10}$.
So its radius is a factor of $10^{8}$ bigger, the area of the column of atmosphere it takes out is $10^{16}$ times bigger (as it's proportional to the radius squared) and the amount of energy deposited is also $10^{16}$ times bigger.
The marble would therefore deposit $7 \mathrm{x}10^{-6} \text{J} * 10^{16} = 7 \mathrm{x}10^{10} \text{J}$ of energy in the atmosphere, and a similar amount in the first three meters of rock.
Since we're looking at explosive-like effects, let's convert this to tons of TNT. One ton of TNT releases $4.2 \mathrm{x}10^{9} \text{J}$. So, our object would deposit $$(7 \mathrm{x}10^{10} \text{J})(\frac{1 \text{ ton}}{4.2 \mathrm{x}10^{9} \text{J}}) \approx 17 \text{ tons}$$ of TNT in the atmosphere and in the first three meters of soil.
The effects from the atmosphere would be comparable to a sizable meteor fireball. On the ground, the energy from the first few meters will reach the surface, producing an explosion comparable to a few tens of tons of TNT (a very large bomb).
Anything deeper than a few tens of meters would produce a relatively short-range surface rumble, like a small earthquake, but relatively little energy will reach the surface.
The same effects would happen at the exit site but in reverse order. The diameter of the earth is about $12700 \text{km}$, and the object is moving at $370 \text{km} / \text{s}$, so if the object comes down vertically, the exit event would happen $12700 / 370 \approx 34$ seconds after the first impact.
tiny but immovable object in space
That makes no sense based on science - so unless you provide us with the physics for your fictional universe, we cannot answer. In the end it is completely up to you. $\endgroup$