If there are two graphs whose shape is isomorphic to each other but whose combination of color used in each vertex is not isomorphic to that of other graph, how can I call their relationship? Should I simply say that they are isomorphic because their shapes are so? Or should I say that they are not isomorphic because their coloring distinguishes them?
The word isomorphic requires context: isomorphic as what? Because graphs are such a fundamental mathematical object, mathematicians might assume it to mean isomorphic as graphs if no context were specified and it was used in talking about graphs, even vertex-colored ones.
As you probably know, two graphs $G$ and $G'$ are isomorphic as graphs if there's a one-to-one and onto function $\phi$ from $V(G)$, the vertices of $G$, to $V(G')$, the vertices of $G'$, with the property that $(v_1,v_2)$ is an edge of $G$ if and only if $(\phi(v_1),\phi(v_2))$ is an edge of $G'$.
If you wanted to, you could define the stronger notion isomorphic as vertex-colored graphs as follows: Two vertex-colored graphs $G$ and $G'$ with colorings $c$ and $c'$ respectively (functions from the vertices to a color set) are isomorphic as vertex-colored graphs if there are one-to-one and onto functions $\phi$ from $V(G)$ to $V(G')$ and $\pi$ from the vertex colors of $G$ to the vertex colors of $G'$ where both i) $(v_1,v_2)$ is an edge of $G$ if and only if $(\phi(v_1),\phi(v_2))$ is an edge of $G'$, and ii) $c'(\phi(v))=\pi(c(v))$ for each vertex $v$ of $G$.
From your description, I think you can call your graphs isomorphic as graphs but "not isomorphic as vertex-colored graphs." Note that while most mathematicians would probably understand isomorphic as vertex-colored graphs and define it in the same way, it's not a standard term. The cautious approach is to avoid saying isomorphic (as opposed to isomorphic as specific-things) if there's more than one possible kind of isomorphism.