Surely permenant markers are the way to go. Available now in all colours, including special shades for flytyers. So easy and saves a fortunes sometimes buying many colours of materials.

You can colour threads, foam, shellbacks etc etc, just with the dab of a pen.

You can buy ones with two sizes of tips, in fact pentone make one with three sizes of tips. I now use the permenant washable fabric marker pens. They are available in hundreds of colours and are much cheaper than the ones sold especially for flytyers.