Making cream cheese from raw, non-homogenized milk, what to do with the cream?
In all cheese making and especially with young cheeses like cream cheese, fat adds a lot to the flavor and texture.

You can skim off extra fat but your cheese will be thinner and less richly flavored.

Shaking the cream in won't help if you are using a fermented method (as opposed to using boiling and acid to curdle the milk) because it will separate out again during the fermentation.

Your thickened, fermented milk will be richer on top where the cream rose. It will mix back in when you drain the cheese and form it.