Boundary Length Modifier vs. Zone Boundary Cost.
In standard Marxan, the Boundary Length Modifier (BLM) is a parameter used to control the spatial compactness of solutions (compact versus fragmented solutions).
Standard Marxan
The BLM works the same way in Marxan with Zones, but you also have the option prescribe the spatial relationship between zones. This is useful to encourage further separation of conflicting uses (e.g., separate a forestry zone from a protected area zone) or to cluster zones which share compatible management objectives (e.g., place a buffer zone that is partially protected adjacent to a conservation zone that is fully protected).
Marxan with Zones
Costs applied to each zone relationship
Because Zones 1 and 3 have a high cost between them, they are buffered by Zone 2.
Defining the configuration of the BLM and the Zone boundary relationships is somewhat subjective and requires trial and error. Normally the user will visualize the solutions and try a few different combinations until they are satisfied with the results.