It does not matter for the PCB fabricators how the PCB software is configured (unless you want to send the work file to them), they need only four gerber files for the copper layers plus solder masks top/bottom and optional silkscreens. Rest is pretty irrelevant, although there might be some recommended practices with particular software where the PCB layers should be located internally. For example in PADS, copper layers are always 1 to n, where n is the number of PCB layers. 1 is the top layer and n is the bottom.
Regards,
Janne