If a person plans on eating a bagel with cream cheese, is it better to make hamotzi on the bagel (and eat some) and then cut it and put cream cheese in or should one make it taste better and put the cream cheese in first and then make hamotzi?
It is better to make the berachah on the complete bagel, and only then to slice it and spead the cheese.
As a general rule, shalem (a whole item) takes precedence over chaviv (something that one prefers), a ruling already found in the Tosefta (Berachos 4:11), and cited by Tosafos and the Rosh (Berachos 39b).
In this case, the chaviv is not even in front of us, but one has the option of making the bagel more chaviv by adding the cream cheese. Because the virtue of shalem is greater than that of chaviv, this is not the right thing to do, and one should only cut the bagel after making a berachah and eating some.