It's pretty simple, you cut a piece of foil about the same size as the mold, open the mold, place the foil in between the open halves, clamp the mold shut, now shoot the mold like normal. The foil will split the bait in half, place half the bait back in the mold and shoot your second color.
As far as Essential Series molds vs CNC, I would get a sample pack of baits from Do-It so you can see both up close. I will say I have been fishing ES Senkos all summer and have caught plenty of fish, to me CNC mold baits will catch more fisherman but ES mold baits will catch just as many fish.