This notation already doesn't make sense to me. The right-hand side is OK, but not the left-hand side. I assume that y is a function. In that case, y(x) is a member of its codomain. The left-hand side should probably be F[y]. Note that the right-hand side doesn't depend on x.
I don't understand what you're supposed to do. Is the task just to find the functional derivative of this F? Do you know what the answer is supposed to be?
This notation is only used for the Dirac delta. But in expressions like δF[y]/δy, the delta has nothing to do with any of those, and is more like a ∂.
As I said in my previous post, when I took a course like the one you seem to be taking now, the teacher was completely unable to make sense. I eventually came up with a way to deal with these things that seemed to make sense. I would interpret 0=δF[y]/δy as
$$0=\left.\frac{d}{d\varepsilon}\right|_0 F[y_\varepsilon],$$ where ##y_\varepsilon## is a function for each ε in some interval that contains 0. I would also write y instead of ##y_0##. This is not the proper way to define functional derivatives, but I was at least able to use this to make
some sense of what the teacher was doing. (I never did it rigorously though).
Let's try it with your problem: (I'll use t instead of ε to save myself some time).
\begin{align}
\left.\frac{d}{dt}\right|_0 F[y_t] =\int \left.\frac{d}{dt}\right|_0\left(y_t(x)y_t'(x)+y_t(x)^2\right)\,\mathrm dx =\int\left( \left(\left.\frac{d}{dt}\right|_0 y_t(x)\right)y'(x)+y(x)\left.\frac{d}{dt}\right|_0 y_t'(x)+\left.\frac{d}{dt}\right|_0 y_t(x)^2\right)dx
\end{align} This is at least similar to what you're supposed to get in the first step. I suspect that the numerator you wrote as ##\delta(x)## should just be ##\delta##. If y vanishes at the endpoints of the interval we're integrating over, the second term will actually cancel the first term, so we get
$$\int\left.\frac{d}{dt}\right|_0 y_t(x)^2\,\mathrm d x.$$ The actual definition of functional derivative is included in Arnold's book, p. 55-56.
http://books.google.com/books?id=Pd8-s6rOt_cC&lpg=PP1&hl=sv&pg=PA55#v=onepage&q&f=false