Whatever your system, no matter. This is not about how one keeps his or her kitchen. However, if you have more than one towel, let me suggest a tip for keeping them organized.
Try initial monogrammed towels to keep your kitchen towels apart, easily. For example, get a D for your dishes, or an H for your hand towels. (And now, the title makes sense). If one is a strict adherent to his or her system, there is an added benefit. The alphabetic drying apparatuses make it easy for guests to remember which cloth to use, and when.
19 Twenty Apartments has a brilliant tutorial on simple, chic, monogrammed towels. I would buy these somewhere. I am glad I found the site instead. If you are looking to buy, not DIY (and who doesn't sometimes?) please support a fellow DIYer if you can. Check out these great towels on Etsy, where you can get custom goods and support a fellow artist.