[guided]We first spell out the quotient structure because every later formula depends on using the same convention. The mapping torus $T_f$ is the quotient of $F\times\mathbb{R}$ by the action
\begin{align*}
\rho:\mathbb{Z}\times(F\times\mathbb{R})&\to F\times\mathbb{R}, & \rho(n,(y,t))&=(f^n(y),t-n).
\end{align*}
Let $q:F\times\mathbb{R}\to T_f$ be the quotient map defined by
\begin{align*}
q(y,t)=[y,t].
\end{align*}
The action is smooth: for each $n\in\mathbb{Z}$, the map
\begin{align*}
F\times\mathbb{R}&\to F\times\mathbb{R}, & (y,t)&\mapsto (f^n(y),t-n)
\end{align*}
is a product of the diffeomorphism $f^n:F\to F$ and a smooth translation of $\mathbb{R}$. The action is free because if
\begin{align*}
\rho(n,(y,t))=(y,t),
\end{align*}
then $t-n=t$, so $n=0$. The action is proper because the translation action of the discrete group $\mathbb{Z}$ on $\mathbb{R}$ is proper and the projection
\begin{align*}
F\times\mathbb{R}&\to\mathbb{R}, & (y,t)&\mapsto t
\end{align*}
is equivariant for the two translation actions. Therefore the quotient-manifold theorem for free proper smooth actions of discrete Lie groups gives a smooth structure on $T_f$ for which $q$ is a smooth covering map. In this quotient, the equivalence relation is generated by
\begin{align*}
(y,t)\sim(f^n(y),t-n)
\end{align*}
for $y\in F$, $t\in\mathbb{R}$, and $n\in\mathbb{Z}$.
The map $\pi:T_f\to S^1$ is well-defined because equivalent representatives have the same image. Indeed, for every $n\in\mathbb{Z}$,
\begin{align*}
e^{2\pi i(t-n)}=e^{2\pi i t}e^{-2\pi i n}=e^{2\pi i t}.
\end{align*}
Thus replacing $(y,t)$ by $(f^n(y),t-n)$ does not change $e^{2\pi i t}$.
Now we choose representatives in two angular coordinate intervals. Let
\begin{align*}
U_0&:=S^1\setminus\{-1\}, & U_1&:=S^1\setminus\{1\},
\end{align*}
and define
\begin{align*}
I_0&:=\left(-\frac{1}{2},\frac{1}{2}\right), & I_1&:=(0,1).
\end{align*}
The coordinate map $\theta_0:U_0\to I_0$ sends $e^{2\pi i s}$ to the unique $s\in I_0$, and $\theta_1:U_1\to I_1$ sends $e^{2\pi i s}$ to the unique $s\in I_1$. These are smooth coordinate maps on the two open arcs.
Fix $j\in\{0,1\}$ and $[y,t]\in\pi^{-1}(U_j)$. Since $\pi([y,t])\in U_j$, there is a unique $s_j\in I_j$ such that
\begin{align*}
e^{2\pi i s_j}=\pi([y,t])=e^{2\pi i t}.
\end{align*}
Hence $t-s_j\in\mathbb{Z}$. Define $n_j:=t-s_j\in\mathbb{Z}$, so $s_j=t-n_j$. Applying the quotient relation with this integer gives
\begin{align*}
[y,t]=[f^{n_j}(y),t-n_j]=[f^{n_j}(y),s_j].
\end{align*}
The uniqueness of $s_j\in I_j$ gives uniqueness of $n_j=t-s_j$, and then the fibre representative is forced to be $f^{n_j}(y)$. Thus every point of $\pi^{-1}(U_j)$ has a unique representative of the form $(y_j,s_j)\in F\times I_j$. This uniqueness is the reason the local trivialisation will be independent of the initially chosen representative $(y,t)$.[/guided]