Let $\infty$ be the "category" of all categories, where the objects are categories and the morphisms are functors. I am trying to motivate the definition of equal categories by doing it as follows.
We say two categories are equal $C=D$, or isomorphic, if there exist functors $F:C\to D$ and $G:D\to C$ such that $G\circ F = \text{id}_C$ and $F\circ G = \text{id}_D$. By $=$ of functors, we mean equality within the category of functors, i.e. $G\circ F = \text{id}_C$ in $\text{Fun}(C,C)$ and $F\circ G = \text{id}_D$ in $\text{Fun}(D,D)$. Thus, there exist natural transformations $\varphi: G\circ F \to \text{id}_C$ and $\psi: F\circ G\to \text{id}_D$ which are isomorphisms.
How does one use this approach to show that it leads to the standard definition of equal categories? (i.e. $F(\varphi_A) = \psi_{F(A)}$ and $G(\psi_B) = \varphi_{G(B)}$).
I think you are confusing three different notions here.
Notation: $A=B$.
Notation: $A\cong B$.
Notation: $A\simeq B$.