The design and implementation of dopant-based silicon nanoscale devices rely heavily on knowing precisely the locations of phosphorous dopants in their host crystal. One potential solution combines scanning tunneling microscopy (STM) imaging with atomistic tight-binding simulations to reverse-engineer dopant coordinates. This work shows that such an approach may not be straightforwardly extended to double-dopant systems. We find that the ground (quasi-molecular) state of a pair of coupled phosphorous dopants often cannot be fully explained by the linear combination of single-dopant ground states. Although the contributions from excited single-dopant states are relatively small, they can lead to ambiguity in determining individual dopant positions from a multi-dopant STM image. To overcome that, we exploit knowledge about dopant-pair wave functions and propose a simple yet effective scheme for finding double-dopant positions based on STM images.