The first part of your sentence is missing, so we have to guess what you want to know. As it stands, it could also mean the method of making pastry by rubbing in the butter with the flour.

What is the full of sentence with that phrase you want to ask?So we can understand it like this: *"way to rub it in" means"how to emphasize or repeat an embarrassing fact" ("way" here means "how to...",it sounds "one's habitual action") Example:Her daughter has won the first prize many time in the Olimpic so she's very proud and happy."Do you know i have a genius?" and that's way to rub it in about her happiness... (Do you understand?)

Don't rub it in: Don't keep going over your point over and over again. I'm already feeling stupid because you have won the argument already. Maybe they have found several "ways to rub it in", they have found several arguments that make the person feel even more and more stupid or stressed. In this case they are "really rubbing it in".

way here means a mean, an option, a process. or even can mean a solution.