In Prusa Slicer, do the following:
Printer Settings > General
Increase the number of extruders to the number of colors you want to use in a print.
Printer Settings > Custom G-code
M600 to Tool change G-code
Click the “Add” Button
Add the STL files for ALL colors. Click “Yes” for the following:
Order the colors and extruders in the right pane in which you want to print first.
Once sliced it should look like the following:
Credit to Malolo on Thingiverse. This is a great example of how to do multi-color prints using a single extruder. Also, his Raspberry Pi cases are my favorite.