I'm finishing a course on basic abstract algebra, which covers groups, rings, modules, and finite group representations. However, up to this point, I am not very sure about the concept of isomorphism.
I know there are examples where given a group $G$ and two normal subgroups, $H$ and $K$, where $H \cong K$, but $\frac{G}{H} \not \cong \frac{G}{K}$. For instance, see here. However, for (external) direct sum, this does not seem to be a problem, for groups $A,B,C,D$, if $A \cong B$, $C \cong D$, $A \oplus B \cong C \oplus D$.
I only know a little (if not nothing) about category theory. When learning general topology, we constructed product topology and quotient topology with universal product, and that's the most I know about these constructions.
So my question is, when we create a new object based on two or more objects in the same category, does the isomorphism carry over? For instance if we make object $(AB)$ from $A$ and $B$, and $(CD)$ from $C$ and $D$, when can we conclude that $A \cong C$, $B \cong D$ implies that $(AB) \cong (CD)$, or vice versa?
This is answered by the concept of a functor. Notice that every functor $F : \mathcal{C} \to \mathcal{D}$ has the fundamental property $$A \cong A' \implies F(A) \cong F(A')$$ for all objects $A,A'$ in $\mathcal{C}$. Whenever you encounter a statement such as "if ... are isomorphic, then ... are isomorphic", it is usually a consequenc of this general result.
For example, the direct sum of abelian groups is a functor $$F : \mathbf{Ab} \times \mathbf{Ab} \to \mathbf{Ab},~ (A,B) \mapsto A \oplus B,$$ with the evident definition on morphisms. It follows that if $(A,B) \cong (C,D)$ (which is clearly equivalent to $A \cong C \wedge B \cong D$), then $A \oplus B \cong C \oplus D$.
The counterexample with quotient groups that you mentioned happens essentially because $H \mapsto G/H$ is not a functor on the category of groups that happen to be normal subgroups of $G$. It is a functor when you restrict the morphisms to inclusions, since any inclusion $H \subseteq H'$ induces a homomorphism $G/H \to G/H'$. So $G/(-)$ is a functor in this sense, but this only gives us $H = H' \implies G/H \cong G/H'$ what is not very interesting.
More interesting is the following category $\mathbf{Grp}_{\mathrm{sub}}$. Its objects are pairs $(H,G)$ where $G$ is a group and $H$ is a normal subgroup of $G$. A morphism $(H,G) \to (H',G')$ is a homomorphism of groups $f : G \to G'$ with $f(H) \subseteq H'$. There is a functor $$Q : \mathbf{Grp}_{\mathrm{sub}} \to \mathbf{Grp},~ (H,G) \mapsto G/H$$ with the evident definition on morphisms: any homomorphism $f : G \to G'$ with $f(H) \subseteq H'$ extends to a homomorphism $[f] : G/H \to G'/H'$, defined by $[f] \circ \pi_H = \pi_{H'} \circ f$.
So the fundamental property shows that $(H,G) \cong (H',G')$ implies $G/H \cong G'/H'$. Here, the relation $(H,G) \cong (H',G')$ means precisely that there is an isomorphism $f : G \to G'$ with $f(H) = H'$. This is the correct replacement of the counterexample mentioned in the beginning.
And this special case is also useful in practice. To give a simple example, consider the isomorphism $2 : \mathbb{Z} \to 2\mathbb{Z}$. It maps $2 \mathbb{Z}$ onto $4 \mathbb{Z}$. As a consequence, $\mathbb{Z}/2\mathbb{Z} \cong 2\mathbb{Z}/4\mathbb{Z}$.