I'm not sure what you mean by join together the shapes. I assume you mean you want a single torus but at different spots on the torus you want one of either geometry to shine through more. Assuming that parametrisation of the Torus is approximately the same (same $(u,v)$ values map to points close together). Then you could try the following:
Assuming both cylinders have some parametrisation $R^2 \rightarrow R^3$ with $(u,v) \in [0,1]$. We then have two tori: $T_1(u,v)$ and $T_2(u,v)$. Then we can combine these together with additional blending functions $\alpha(u,v)$ and $\beta(u,v)$ which have the following properties: $\alpha(u,v)$ + $\beta(u,v) = 1$ and $\alpha(u,v)$, $\beta(u,v) \in [0,1]$. Then we can create a blended torus:
$$T_b(u,v) = \alpha(u,v) T_1(u,v) + \beta(u,v) T_1(u,v). $$
Naturally, the question is what are these functions $\alpha$ and $\beta$ and that is what you have to decide yourself. If you do not really care about where exactly the blend is done you can set $\alpha$ to be determined by a Perlin noise function and then setting $\beta = 1 - \alpha$. If you require more customization you could try to create a custom height map or create a grid of Bezier patches on the UV plane. Having half of the torus as $T_1$ and the other as $T_2$ you could use just $$\alpha(u,v) =
\begin{cases}
1-2u, & u \in [0, 0.5]\\
2u - 1, & u \in [0.5, 1]\\
\end{cases}
$$ and once again $\beta(u,v) = 1 - \alpha(u,v)$ (assuming they are both parametrised with $u$ along the toroidal direction). You can create smoother blends by using smoother blending functions.
