You can set the "Build Active Architecture Only" and "Archs" values from command line itself. We set ARCHS="armv7 armv7s" ONLY_ACTIVE_ARCH=NO.
Eg
/usr/bin/xcodebuild ARCHS="armv7 armv7s" ONLY_ACTIVE_ARCH=NO -workspace -scheme ......
This will free you from manually changing the values in your project settings.