A wide variety of emerging functional materials reveal their physical properties determined by electronic inhomogeneities appearing at varying length scales. Here, some of our recent studies using extended x-ray absorption fine structure (EXAFS) and space resolved photoemission on self-doped BiS$_2$-based superconducting systems will be presented. Space resolved photoemission shows metallic phase embedded in the stoichiometric CeOBiS$_2$ and EuFBiS$_2$. While bulk of the sample is semiconducting, the embedded metallic phase is characterized by the Fermi surface similar to the one of doped metallic BiS$_2$-based materials. The results will be discussed in connection with peculiar local structure with axial Bi-S atomic displacements being important for the self-doping.