I've been trying to figure out how to change what part of an image the UI LAYO files link to.

for example, "S3_2F7D0004_00000000_D4C492FE84FF892E_ATLAS_GameEntryMainMenu_00%%+IMAG" has many UI textures on it for each element but changing them around messes up the mapping of the texture, and changing the "Area" values in LAYO file just moves it around the screen not remapping where the texture comes from.

Any help on how I can change around the part of the image they look to would be appreciated!

I don't know how they are linked. I use scripting to change the main menu elements. Each object in the layout file has a ControlID. Some of them are zero, but others have a unique value. Converting them from hexadecimal to decimal, you can search for them in UI.dll, in MainMenu class, and see how are they being used.