Say $G = \langle x \rangle$ and $H = \langle y \rangle$ are cyclic groups of order $n$. These are isomorphic, and the isomorphism has the form $f(x^i) = y^i$.
My question is as follows. I don't want to define this map only for $0 \leq i < n$ because then if I want to prove that $f(x^i y^j) = f(x^i) f(y^j)$, I'd have to construct $x^{i+j}$, and it may be the case that $i + j > n$.
It's clear to me every element of, say $G$, can be written uniquely as $x^i$ if $0 \leq i < n$, but if I allow $i$ to range over all of $\mathbb{Z}$, it is not unique. Would this require me, for a fully rigorous proof, to prove that the map $f$ is well-defined? That is, would I need to show that if $x^i = x^j \in G$, then $y^i = y^j$?
You are correct to say that for a fully rigorous proof we must show that $f$ is well-defined, that is, if $i,i'\in \Bbb Z$ and $x^i=x^{i'}$ then $y^i=y^{i'}.$
For any $a,b\in G$ there are unique $i,j\in\{0,...,n-1\}$ such that $a=x^i$ and $y=x^j.$ So $f(a)f(b)=y^{i+j}.$ If $0\le i+j\le n-1$ then $f(a)f(b)=f(ab).$ If $i+j\ge n$ then $i+j-n \in \{0,...,n-1\}$ so by def'n of $f$ we have $f(a)f(b)=y^{i+j}=y^{i+j-n}=f(x^{i+j-n})=f(x^{i+j})=f(ab).$
BTW. You used $y$ to denote a generator of $G'$ but later used $y$ to denote a member of $G$. This is bad style, as it can lead to confusion.