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The page headers and footers use the string sets defined for publication, chapter, and section titles. These string-sets are defined in the numbering CSS:
Set to the title of the current part (only for DITA bookmaps that use parts).
Set to the title of the current chapter (Shallow and Deep numbering).
Set to the title of each section (Deep numbering only).

Although you may define string sets in your customization CSS, you need to take into account the fact that the string-set CSS property is not additive, and matching the same elements will end up breaking the current definitions. A very common use-case is to match the title element that is also used in the default CSS. The best approach in this case is to take a look at the rules from the numbering CSS, copy the ones dealing with string sets to your customization, then alter the property definition by adding your definition to the existing ones (and not removing the existing ones).