I cannot find an authoritative resource that describes how to estimate base drag for a missile or space launcher during powered flight. There are plenty of resources that describe how to estimate the common types of drag (form, induced drags) but nothing reliably describes base drag. Some papers are even contradictory.
FYI: Base drag is most commonly seen in the empty space behind the base of an artillery shell in flight. The air in this space forms a recirculation zone at lower than ambient pressure. This lower pressure acts like a drag force. Some shells even have a small rocket engine just to fill in this pressure to reduce overall drag and increase range. For rockets, if the stage diameter is bigger than the nozzle of the rocket, there is an annular base drag zone. Many people ignore it but some calculations show it may not be trivial depending on design. Some simulation models even give unphysical results (like discontinuites in speed). Of course, after flight tests everyone ignores the simulation estimates and models from the flight data -- if they get enough data.