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.
Best regards and tight lines
Mick Porter