I don't know where you read that, (I didn't do it to break in either of my Reef Octopus skimmers.)
I just put it in the sump, and set it like the instructions mentioned (with the bubbles half way up the cone). I installed mine during cycling, so maybe that is why I didn't sense any "break-in period" with either one, but just checking it every day twice or so for the first weeks, and making gradual adjustments to keep the bubbles where you want them worked for me.
Of course, your mileage may very.