Let's say for the function $x^2+y^2=25$.
Taking the differential of $x^2$ and $y^2$, we have $2xdx+2ydy=0$
Then we end up with ${dy \over dx}=-{{x \over y}}$
My question is when talking about derivatives $dy \over dx$ should be taken as a whole, but here we end with the same notation, should I perceive ${dy \over dx}=-{{x \over y}}$ as y's derivative with respect to x as well?
Yes. It is the derivative of $y$ w.r.t. $x$. In fact you could have done it this way. Take the derivative w.r.t. $x$ on both sides. Then $$2x+2y\frac{dy}{dx}=0$$ $$\frac{dy}{dx}=-\frac{x}{y}$$