If I have point $A$ at $(0,0)$ and point $B$ at $(2,2)$, each with a mass of 100, I think I need to calculate the final force first $\frac{GMm}{r^2}$ and then work out the components of that force that go in the x and y direction.
Or can I just multiply the final force by the $ \Delta x$ or the $ \Delta y $?
Using your formula for gravity you will find the force between them, along the vector $(2,2)$.
If you want to calculate the components in the x- and y-direction, you can use for example Pythagoras' theorem (the length of the hypotenuse is the force calculated).