I'll assume you are referring to the new Do-It system. I have it and find it easier to have the two cups of color side by side and pull the plastic into the cylinders at the same time. I keep the injectors pointing down while I fit the block back into place and tighten the wing nut... Then I tip the until straight up and gently push in the plungers just until both colors of plastic show, quickly wipe off any excess then fit the nozzle in the mold and shoot it. I've never been big on pulling the nozzle and pouring plastic in to the cylinder and as long as the nozzle is kept pointing down any air that might sneak into the cylinder and plastic will rise up as a bubble so voiding air is no issue.
More than anything, its whatever you are comfortable with. Develop a system that works cleanly, SAFELY, and efficiently for you and go to work.