Use the colors the system selects. Please think of the system like it's a painter, and the thread set 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 colors changes the other colors perceived colors.
To make the system use your thread inventory, create a Thread Set with just the colors from your inventory. Give the painter your paints (thread set) and ask it to paint (digitize) you a picture.
The thread brands you can it use are ThreadArt, Isacord, Madeira Poly, Madeira Frosted Matt, Gunold Poly and Gunold Sulky