The Swapper3D doesn't know what material or color is in a particular nozzle, what it does know how to select a QuickSwap-nozzle from a particular receptacle and load it on demand from the 3d printer. You need to keep track of colors and materials in Prusa Slicer. Whichever tool you assign to a particular part of your print, either a body or a feature Prusa Slicer will call the swap command for that particular nozzle, at the correct time in the print and all of that is in the gcode file that Prusa Slicer exports. Just like you would normally do for an mmu print.