How do you use those skins in stock maps? For example, I've edited the rep side to change the 501st blue colour to the yellow colour seen on obi's army.

How can I load that onto, say the Utapau map to make it more movie accurate?

If you want to put custom skins into a custom map that you've made, see this tutorial. If you want to put those skins onto stock Utapau, you'll be creating a side mod or an era mod, depending on your preference. A side mod just replaces the stock side .lvl files in GameData\data\_lvl_pc\side with the custom ones you munged in your map. An era mod requires a bit more explanation:
Era mod tutorial

And as with anything modding related, be sure to check this thread (and use the search function) to see if your question has already been answered.

And I see you're new, but I haven't welcomed you yet. Welcome to GT!