Use the colors the system selects.
One way to think the system is like it's a painter and the thread is the paint but it useing tricks of the eye to mix colors in your brain. Changing colors can has detrimental effects. When you change colors you change the perceived color of other colors.
Your selected thread set is the paint the system can use to when you digitize a project.
Want to make the system use your thread inventory, create a New Thread Set with just the colors from your inventory.