In a paper I was reading, the define a set $Q=(0,T)\times \Omega$, where $\Omega \subset \mathbb{R}^n$ is a bounded domain, and then they write $$\langle \frac{d}{dt}u - \Delta u, \varphi \rangle_{\mathcal D^*(Q), \mathcal D(Q)} = -\langle u, \frac{d}{dt}u \rangle - \langle u, \Delta \varphi\rangle$$ where $\varphi \in C_c^\infty(Q)$ and the duality pairing on the LHS here is between $\mathcal{D}^*(Q)$ and $\mathcal{D}(Q)$. I guess this is just using the definition of the distributional derivatives $D_1, ... ,D_n$ and $D_t$.
Suppose now that $\Gamma$ is a hypersurface and set $S=(0,T)\times \Gamma$. Does the following make sense in some way: $$\langle \frac{d}{dt}u - \Delta_\Gamma u, \varphi \rangle_{\mathcal D^*(S), \mathcal D(S)} = -\langle u, \frac{d}{dt}u \rangle - \langle u, \Delta_\Gamma \varphi\rangle$$ where $\Delta_\Gamma$ is the Laplace-Beltrami operator not the standard Laplacian. How to make this rigourous and precise? I tried searching for distributions on manifolds but that means something else it seems. Any references to this topic are appreciated.
This is indeed the definition of distributional derivatives.
The book "Heat Kernel and Analysis on Manifolds" by Grigoryan (I can even access that part as a free preview on books.google.com) contains formula (7.30): locally integrable function $u(t,x)$ satisfies the heat equation on a manifold $N=(0,\infty)\times M$ in a distributional sense if and only if for every $\varphi \in {\cal D}' (N)$ it holds: $$\left( u, \partial_t \varphi + \triangle_\mu \varphi \right)=0.$$ This is transformed (using Fubini's theorem) in the form (7.31) $$\int_{\mathbb{R}_+} \left( u, \partial_t \varphi\right)_{L^2(M)}dt +\int_{\mathbb{R}_+} \left( u, \triangle_\mu \varphi\right)_{L^2(M)}dt=0.$$ The point in using $L^2$ inner product instead of a duality pairing lies in the fact that for every $t>0$ the solution is a smooth function, no matter what the initial data are. Frankly, I don't understand all the technical details, however, that book might be a worthy reference.