As far as I know, there is no current way to quickly change all composition methods to 0. The best way to avoid this in the future is by setting the composition method to 0 on the first swatch before you add more swatches. Since adding swatches works like copy and pasting, the composition method will already be set at 0, so you won't have to go into the Warehouse and manually change each composition method.
As for skin details, it solely depends on what type of skin detail you're making. For example, if you're making a skin detail that completely overrides the skintone of the sim (example here), you'll need to set the composition method to 0. From what I've noticed, makeup still seems to be able to work with skins set to 0.
I've also noticed that skin details that overlay over the sim's skintone/skinblends (example here) usually have a composition method of 3, so that it goes over the base game skintones, but allows makeup to appear on top of the skin.
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