How can one quickly estimate interference drag for a configuration?
Use Sighard Hoerner's Fluid Dynamic Drag. It lists tons of wind tunnel and flight test data for a wide variety of configurations and flight regimes.

Interference drag has several sources:


Flow separation due to the coincidence of the pressure rises of two bodies. Each of them by itself would show attached flow, but in the vicinity of a similar body with its own pressure rise, the flow separates. This is most pronounced at low speed.
Addition of the accelerated flow of two bodies in transsonic flight. While each of the single bodies has no supersonic pocket around it, both in combination will cause a local supersonic area with a subsequent shock.
Disturbance in the spanwise lift distribution, such as wings interrupted by the fuselage or engine nacelles.


Look for areas where one of these conditions is fulfilled, and then try to find a similar case in Horner's book to estimate its severity. Note that all interference drag varies with speed and angle of attack. Doing so carefully will bring you within 10% of the real drag, but needs some experience.

In the end, drag estimation is like bookkeeping. You need to carefully add each component and make sure to avoid double-counting or mixing up reference areas. Sorry, but if you want a good result there are no shortcuts.