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I can't figure out what that little selection box is under the colour sliders to the right. I've been switching between the two options and trying everything to compare it but I never notice anything different.

Hey, this is quite subtle. It toggles the blending mode of your selection between alpha blending and replacing the alpha values of the underlying image. There will only be a difference if your selection contains pixels with an alpha value less than 255. 

Hope that answers your question! :)

Yep, now I get it. Thanks!