$\frac{dy}{dx}$ is the rate of change of with respect to $x$. I will try to explain what this mean.
For example let us take $y=x^2$
And we are going to find out $\frac{d}{dx}(x^2)$.In other words we are going to find out rate of change of $x^2$ with respect to $x$. In other words we are going to find out how $x^2$ is changing when we introduce a change in $x$.
So, we introduce a change in $x$, say by an amount $h$, so as to make it $x+h$.Now instead of $x^2$ we have $(x+h)^2$. So how much change has been added to $x^2$?.
It is $$(x+h)^2-x^2=2xh+h^2$$
This is the amount change in $x^2$ when we introduced a change of $h$ in $x$.So what is the rate? It is
$$\frac{\text{change in }x^2}{\text{change in }x}=\frac{2xh+h^2}{h}=2x+h$$
Now we note that the rate is dependent on how much change we are introducing.Actually we are not interested in large amount of change. What we want to find is an instantaneous rate of change, we want to to make the change or $h$ as small as possible,as close to zero as possible, but obviously not zero(then there would be no change!). So that $2x+h$ is is getting closer to $2x$ as $h$ gets closer to zero.
We formally write this as
$$\underset {h\rightarrow 0}{lim}\text{ } 2x+h=2x$$ .
Now the formal definition of derivative,
$$\frac{d}{dx}(f(x))=\underset {h\rightarrow 0}{lim}\frac{f(x+h)-f(x)}{h} $$or
$$\frac{dy}{dx}=\underset{\Delta x\rightarrow 0}{lim}\frac{\Delta y}{\Delta x}$$
where $\Delta y$ is the change in $y$ as we change $x$ by $\Delta x$ .
So as $\Delta x$ gets closer to zero $\Delta y$ is also getting zero.Now we may view the derivative as ratio of two infinitesimals. This is the reason why, for instance when $\frac{dy}{dx}=2$ ,we write $dy=2dx$ . This is often useful for practical point of view. But it is not very mathematically rigorous, but one need not be worried about it most of the cases.
It must be clear now that derivative involves concept of limits, and I have explained it in a loose way.But that is okay to understand and to have a feel of what derivative is.
Now coming to your question of differentiating $y^3$ with respect to $x$, Since $y$ is a function of $x$ $y^3$ is also a function of $x$. So it should be possible to do the differentiation using the definition of derivative above.Now if you know $\frac{dy}{dx}$ there are rules known as chain rule to compute the derivative of some function of y with respect to x.But everything is basically derived from the base definition. So just for the sake of completeness
$$\frac{dy^3}{dx}=\frac{d(y^3)}{dy}\frac{dy}{dx}=3y^2\frac{dy}{dx}$$
$\frac{dy}{dx}$ is the same as $\frac{d}{dx}(y)$.
Also when you write $du=2xdx$ what it means is that the infinitesimal change in $u$, when you make an infinitesimal change in $x$ is 2 times $x$ times the infinitesimal change in $x$ .
I may add some more details.Say $y$ is some arbitrary function of function of $x$ ($y=f(x)$).When make change $x$ to $x+\Delta x$, f(x) will change in this way
$$f(x+\Delta x)=f(x)+(\text{some expression in x})\Delta x +(\text{something}){\Delta x}^2+(\text{something else }){\Delta x}^3+......$$
You will see that by using the definition of derivative the coefficient of $\Delta x$ is the derivative of $f(x)$ with respect to $x$. Now $dy$ is ($(f(x+\Delta x)-f(x)$) as $\Delta x$ tends to zero . This can be seen to be equal to $(\text{derivative})\times \Delta x+ \text{other terms}$ as $\Delta x$ tends to zero. What we are doing is almost like ignoring the terms involving higher powers of $\Delta x$ .