Global & Individual Colour Settings
Colour settings/customisations are split into two main types.
Global Colours are a group of colours that have been chosen to reflect a theme's overall colour scheme. You can change the global colour on a theme and the change will affect all instances of that particular colour where it appears on the theme.
Individual Colour Settings are put into groups depending on whereabouts on your theme they are used. For example, the 'product page' colour group will contain individual colour settings for the theme's product page.
When customising the colours on your theme, you can use the global colours setting to customise your theme's overall colour scheme, but then if you want to make individual customisations you can select a particular colour group and choose to specify the colour settings individually (just for that group) which will stop the global colours being used/applied. You can read more about individual colour settings here.
Customising Global Colours
On clicking into the colours section you'll see the available global colours presented to you for customisation.
To change a colour you can click into the coloured square and choose a new colour from the colour picker.
Alternatively you can enter a new hexadecimal colour reference into the box (indicated on the screenshot below).
When you change the colour setting you'll notice the live website preview change accordingly.
When you've made your change to the colour click the 'ok' button.
When you've finished making all your global colour changes don't forget to save your changes!