I guess it really depends on what your actual system is. If this is a heterostructure, then one should have to study is as bulk configuration, and calculate band structure with Band structure analyzer, FatBandStructure, DOS or PDOS. If it is an interface between two structures, then using device configuration seems to be more adequate, and one can then use, e.g., PLDOS to look at the electronic structure across the interface structure. But you can still do band structure calculation for the central region of such device by treating this central region as bulk configuration, provided that the electrodes do not alter the electronic structure of the central region. So, it is really up to you to investigate and decide what is the best way of approaching this problem.
