Tool positions are counted counter-clockwise from the Probe, as below:
By convention, we have spindles starting from the Tool 1 position, and HT hotends starting from the Tool 5 position.
In the cabinet, Tool 1 is in front and Tool 5 is in back:
By convention, we will start drive assist in positions with the shortest path (Tool 3 first, then 4, then 2 if it has an FDM installed).
Normally the tools corresponds directly between these positions and tool numbers in the controller, Simplify3D, and Fusion360. Occasionally there is some disagreement, most notable "Extrusion factors" on the Job Status screen:
Here, Extruder 0 corresponds to the first extruder installed. In the photos above, that would be Tool 3. Extruder 1 is the second extruder installed, Exturder 2 is the 3rd, and Extruder 3 is the 4th. The 4th extruder installed applies to ALL filament assist drives.