I am trying to find the points of intersection of $y = x^2 -3x$ and $y = 3x^2 - 5x -24$
I first set them equal to each other:
$$2x^2 -2x -24 = 0$$
Then I solved it:
$$\begin{align}x &= 4 \\ x &= -3\end{align}$$
Now as I currently understand you must substitute those two $x$ values into their respective quadratic equations in order to find the $y$ co-ordinate for the points of intersections. E.g
$$\begin{align}fx(4) &= 3x^2 - 5x -24 \\ fx(-3) &= x^2 -3x\end{align}$$
How do I know what $x$ value to substitute into what equation?

It doesn't matter which one you substitute it in since it is a point of intersection, thus the $y$-coordinate of both graphs will be the same.
For example, let's try finding the coordinates of intersection where $x=4$:
$$f(x)=x^2-3x \Rightarrow f(4)=16-12=4$$ Now, let's try this with the other function: $$f(x)=3x^2-5x-24 \Rightarrow f(4)=48-20-24=4$$ Which is the same answer: $(4,4)$.
Here is a graph showing the intersection: