Visit the Bee Lab inside the game

Scroll to the right until you see Trait Swap

Tap Trait Swap

Choose the Bee you want to chanage

Tap "Cosmetic" (above the list of Bees) to choose the cosmetic you want to apply

Tap "Preview" to see how it will look, then "Wear" under the Bee on the left

Congratulations on your new Bee!

CAUTION: If you swap out a trait, any boosts from the old trait will be lost. 

NOTE: Chase Bees, one-of-one Bees, and some Mad Honey Vial Bees are not eligible for trait swap. Learn more here.

When you add both upgrades and cosmetics that include upgrades, here's how the final stat is calculated:

The formula: (Base Stat X Upgrade) + Cosmetic Upgrades = Total Stat

Said another way, upgrades are calculated first and then any additional stats from cosmetics will be added on top.