This paper presents a scalable method for controlling ion crystals in a grid-based surface-electrode Paul trap, enabling the sorting and reordering of multispecies crystals. The method combines coiling of control electrodes at translationally symmetric locations with the ability to exchange voltages applied to two special electrodes gated by a binary input, allowing site-dependent operations using a fixed number of analog voltage signals and a single digital input per site. The technique is demonstrated in two experimental systems containing nominally identical grid traps, one using ${}^{171}$Yb$^+$,$^{138}$Ba$^+$ crystals and the other ${}^{137}$Ba$^+$,$^{88}$Sr$^+$ crystals. The conditional intrasite crystal reorder and conditional exchange of ions between adjacent sites are characterized, achieving subquanta motional excitation in the axial in-phase and out-of-phase modes at exchange rates of 2.5 kHz. The logic controlling the voltage exchange is implemented in software, mimicking a proposed hardware implementation using crossover switches. These techniques can be extended to implement other conditional operations in the QCCD architecture, such as gates, initialization, and measurement. The success of the transport operations confirms the necessary control for multispecies junction transport, despite electrode crowding, and paves the way for large-scale, periodic, 2D ion traps with practical wiring demands.This paper presents a scalable method for controlling ion crystals in a grid-based surface-electrode Paul trap, enabling the sorting and reordering of multispecies crystals. The method combines coiling of control electrodes at translationally symmetric locations with the ability to exchange voltages applied to two special electrodes gated by a binary input, allowing site-dependent operations using a fixed number of analog voltage signals and a single digital input per site. The technique is demonstrated in two experimental systems containing nominally identical grid traps, one using ${}^{171}$Yb$^+$,$^{138}$Ba$^+$ crystals and the other ${}^{137}$Ba$^+$,$^{88}$Sr$^+$ crystals. The conditional intrasite crystal reorder and conditional exchange of ions between adjacent sites are characterized, achieving subquanta motional excitation in the axial in-phase and out-of-phase modes at exchange rates of 2.5 kHz. The logic controlling the voltage exchange is implemented in software, mimicking a proposed hardware implementation using crossover switches. These techniques can be extended to implement other conditional operations in the QCCD architecture, such as gates, initialization, and measurement. The success of the transport operations confirms the necessary control for multispecies junction transport, despite electrode crowding, and paves the way for large-scale, periodic, 2D ion traps with practical wiring demands.