You make the item undyed first. Then you do another synth with just the item and dye as ingredients. This will complete instantly instead of starting the crafting mini-game.

E.g. Undyed Hempen Cloth, Sheep Leather, Hempen Yarn -> Hempen Coif.
Hempen Coif, All-Purpose Grey Dye -> Hempen Coif (Grey)
Got these recipes from mooglebox by the way.