Simply stated, calling for (Actions > Processing) "Balance Splices" will assign either left or right wire entry to each splice based on it's respective location in the bundle structure. All splices should be placed in the bundle structure before running the action to avoid errors. In fact, running the "Balance Splice" process will reveal associated problem areas in the design ("Harness Engineering" tab). If you are using spider diagrams, the diagrams will reflect the resulting orientation.
More information can be found in the Harness User Guide under "Harness Processing".
Hope that helps,