Default [Q] inverted contacts and google dialer

I was hoping someone may know how to do this because other have gotten it to work.
This link has many inverted apps on it. (see page 26 for a blackedout moto x Google dialer zip)

(Many nexus 5 apps work fine on the X) The blackedout MMS works without a hitch however the inverted contacts and dialer are more tricky. I have an (all of them) I'm rooted but have an unlockable bootloader. Flashing does not work for me. Opening the zip I can move
Apks in their respective folders and change permissions. Now this works fine when the zip is only an
apk, however if there are other files like update binary and script I do not have any luck. Looking
online there are a million how two's for using a file browser to install just system apks but not ones that
have extra files in the zip.