Use the thread colors the system selects. Please think of the system like it's a painter, and the thread palette is the paint the system can use when digitizing (painting) a project, but using tricks of the eye to mix thread colors (paint) in your brain. Changing thread color changes the other colors perceived colors.
To make the system use your thread inventory, create a Thread palette with just the colors from your inventory. Give the painter your paints (thread set) and ask it to paint (digitize) you a picture.