The condition of a matrix gives a bound on how inaccurate the solution $\vec{x}$ will be after approximation. So given $A \vec{x} = \vec{b}$, how much does $\vec{x}$ change when there is a change in $\vec{b}$. Here is an example:
$$\pmatrix{1&1\\1&1.001} \pmatrix{x\\y} = \pmatrix{2\\2} \implies x=2, y=0$$ $$\pmatrix{1&1\\1&1.001} \pmatrix{x\\y} = \pmatrix{2\\2.001} \implies x=1, y=1$$
This is an ill-conditioned matrix because a small change in $\vec{b}$ lead to a big change in $\vec{x}$. But here's where I am confused. The matrix $A$ can be considered as observed values or input data. However, I am not sure what $\vec{x}$ and $\vec{b}$ are in this case.
This question isn't really about condition number at all, but rather "how do I interpret a system of linear equations". In general, $A$ is a matrix of coefficients, $\vec{x}$ is a vector of unknowns, and $\vec{b}$ is a vector of constants. The single matrix equation you have above relates to two linear equations in two unknowns. Specifically:
$$x + y = 2$$
and
$$x + 1.001y = 2$$ (or 2.001, depending on which version you are using)
So one (geometric) interpretation of this matrix equation is to find the intersection points between the two lines $y = -x + 2$ and $y = \frac{-1}{1.001}x + 2$. In this sense, the vector $\vec{b}$ represents the y intercepts. Of course, this assumes that your quantities are in $\mathbb{R}^2$ and that you are able to use this interpretation for useful results.
Otherwise, "what do these quantities represent" is answered by "whatever they need to for your application".