The crucial step is that one can always replace a cochain in $K^{**}$ by one with one with last component zero.
To see that $r*$ is onto, take a cocycle in $K^{**}$. By the first remark, this is represented by a pair of forms $(\eta_1,\eta_2)$, and the cocycle condition means in the vertical direction, that each $\eta_i$ is closed, and second, that $\eta_1=\eta_2$ in $U\cap V$. Thus there is a global form $\omega$ that restricts to $(\eta_1,\eta_2)$.
To see that $r*$ is injective, take a global form $\omega$ and suppose the restrictions $(\omega_1,\omega_2)$ have trivial class in $\operatorname{Tot} K^{**}$, so this is of the form $D\varphi$ for some $\varphi$. By the first remark, one can assume $\varphi$ has zero last component. Now $r^*\omega$ also has zero last component -- it has $(q,0)$ component $r^*\omega$ and $(q-1,1)$ component $0$, and because $D\varphi=r^*\omega$, it follows that $\delta\varphi=0$, so $\varphi$ is a globally defined form. But we also have $d\varphi=r^*\omega$, so $\omega$ is exact.
Their proof can be phrased as follows. There is a double complex $C^{**}$ obtained by looking at the exact sequence of complexes as such a double complex:
$$ \Omega^*(M)\stackrel{r}\longrightarrow \Omega^*(U)\oplus \Omega^*(V) \longrightarrow \Omega^*(U\cap V)$$
This is a first quadrant cohomological double complex, and it has exact rows. Now there is induced a map $$r: \Omega^*(M)\to \operatorname{Tot}(K^{**})$$
as described by Bott and Tu. Now one checks the cone of $r$ is exactly the total complex of $C^{**}$, and because $C^{**}$ has exact rows -- by virtue of the exactness of the Mayer-Vietoris sequnce --- its total complex is acyclic. Because $\operatorname{cone}(r^*)$ is acyclic, it follows that $r$ is a quasi-isomorphism, as desired.
So, let us show that if a first quadrant cohomological complex $C^{**}$ has exact rows, then $\operatorname{Tot}(C^{**})$ is acyclic. Write $d'$ for the vertical differential and $d''$ for the horizontal one.
Consider a cocycle $c=(c_{0,q},c_{1,q-1},\ldots,c_{q,0})$. Then $d''c_{q,0}=0$. Because the rows are exact, there is $b_{q,0}$ such that $d''b_{q,0}=c_{q,0}$. Then $c'=c-Db$ where $b=(0,\ldots,0,b_{q,0})$ has last component $0$, and $Dc'=0$. Continue in this way: inductively assume you have killed the last $j$ components, so now $d''c_{q-j,j}=0$, so there is $b_{q-j,j}$ such that $d''b_{q-j,j}=c_{q-j,j}$. Inductively, we reach $c''$ with only the top component $(0,q)$ nonzero. But if $Dc''=0$, this means that $d''_{0,q}c''_{0,q}=0$, and since $d''$ is injective at $(0,*)$ because our complex has exact rows, it follows that $c''=0$. This is exactly what Bott and Tu are doing.