Example of simple scripting of TileMill exports - more details at https://www.mapbox.com/tilemill/docs/manual/exporting/#exports_from_the_command_line

tilemill-scripted-export.sh

#!/bin/bash

# Settings: edit these as needed
PROJECT_NAME="test"
OUTPUT_DIRECTORY="~/Documents/MapBox/export/"

# first change into TileMill code directory
cd /Applications/TileMill.app/Contents/Resources/

# hint: use http://bboxfinder.com/ to get bounds in lon/lat

# first export
BOUNDS="-125.090332,45.336702,-116.147461,49.253465"
NAME="washington"
echo "Exporting $NAME using $BOUNDS to ${OUTPUT_DIRECTORY}/${NAME}.mbtiles"
./index.js export ${PROJECT_NAME} ${OUTPUT_DIRECTORY}/${NAME}.mbtiles --minzoom=0 --maxzoom=4 --bbox=${BOUNDS}

# second export
BOUNDS="-125.551758,41.672912,-116.147461,49.253465"
NAME="oregon"
echo "Exporting $NAME using $BOUNDS to ${OUTPUT_DIRECTORY}/${NAME}.mbtiles"
./index.js export ${PROJECT_NAME} ${OUTPUT_DIRECTORY}/${NAME}.mbtiles --minzoom=0 --maxzoom=4 --bbox=${BOUNDS}

Export names should not have spaces in them.

Can you give an example of uploading the .mbtiles to your mapbox account using export's upload or sync format?