Consider:
$$ dU = T dS - PdV$$
Now, how would I differentiate both sides with temperature...?
Or more simply:
$$ dy = f'(x) dx$$
Can I differentiate this expression above? (I'm not talking about moving dx to the denominator on left)
More particularly:
$$ (dy)' = (f'(x) dx)'$$
does the above expression have any meaning?
I'm not exactly sure of your question, but you can indeed differentiate a differential. It is a slightly different notation, in that the typical notation for a second derivative doesn't allow for this, but if you adopt a different notation for the second derivative, it works perfectly fine. The typical notation for the second derivative of $y$ with respect to $x$ is $\frac{d^2y}{dx^2}$. Using a notation that allows for taking second differentials, this becomes $\frac{d^2y}{dx^2} - \frac{dy}{dx}\frac{d^2x}{dx^2}$.
The process of taking a differential of a differential is straightforward. The differential of a differential (say $dx$) is simply $d^2x$. In other words, $dx$ has the meaning $d(x)$ and $d^2x$ has the meaning $d(d(x))$. The thing to keep in mind is that if you have something like $x\,dx$, this has to be differentiated with the product rule. So $d(x\,dx) = x\,d^2(x) + dx^2$.
So, if you are wanting to differentiate your equation above, you would get:
$$ dU = T\,dS - P\,dV \\ d(dU) = d(T\,dS - P\,dV) \\ d^2U = d(T\,dS) - d(P\,dV) \\ d^2U = T\,d^2S + dT\,dS - P\,d^2V - dP\,dV $$
If you wanted that in terms of a second derivative, you would have to get it in the form of the second derivative I noted above.
You can find out more about using higher order differentials algebraically from my paper, "Extending the Algebraic Manipulability of Differentials."