Conserving biodiversity is principally achieved through the designation of protected areas, guided by the process of systematic conservation planning (SCP). SCP identifies networks of protected areas that represent regional biodiversity. Ecologists, planners, and decision makers may each use different spatial boundaries, scales, and extents for individual projects; these can be misaligned with the jurisdictional scope and scale of management decisions, impacting the effectiveness of resulting conservation actions. Using British Columbia as a study area, we explore how analysis design effects SCP outputs. Using ILP solvers, we measured concordance, efficiency, and equity between the varying extents (ecological and administrative) and scales (fine, coarse, provincial). Higher efficiency but lower equity results when constraints are lifted. Inversely, higher land requirements with higher equity result when constraints are imposed. We show how initial design decisions influence the priority assigned to conservation areas and find insights for striking a balance between landscape-scale and regional-scale analyses.