There are 2 areas in the system in which you can define the 'Skin':
1. On a system level - System Self-Admin < System Settings < System Skins.

2. On a Sub-System level - Settings < Skin. Changes made here will affect the current subsystem only.

This video highlights the customization of the system skin. It provides an in-depth guide on how to change the colors and logos within the system.
Qmarkets Skin Designer Tutorial
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