The understanding of interactions between electrons and phonons in atomically thin heterostructures is crucial for the engineering of novel two-dimensional devices. Electron-phonon (el-ph) interactions in layered materials can occur involving electrons in the same layer or in different layers. Here we report on the possibility of distinguishing intralayer and interlayer el-ph interactions in samples of twisted bilayer graphene and of probing the intralayer process in graphene/h-BN by using Raman spectroscopy. In the intralayer process, the el-ph scattering occurs in a single graphene layer and the other layer (graphene or h-BN) imposes a periodic potential that backscatters the excited electron, whereas for the interlayer process the el-ph scattering occurs between states in the Dirac cones of adjacent graphene layers. Our methodology of using Raman spectroscopy to probe different types of el-ph interactions can be extended to study any kind of graphene-based heterostructure.