There's more than one Touhou manga. In fact, there are a ton of them. Majority of them are doujinshi manga, i.e. fan-made/circle manga.
If you mean -official- manga then there's currently 3 of them. All written by ZUN with commissioned artists doing the artwork:
Silent Sinner in Blue - This is probably what you're talking about. Original story by ZUN. 7 chapters translated.
Inaba of the Earth and Inaba of the Moon - 4koma serialized manga written by ZUN. Pretty entertaining. I think only 4 chapters have been translated.
Little and Eastern Nature Deity/Strange and Bright Nature Deity - Another serialized manga that features exclusively the Three Mischievous Fairies known as Sunny Milk, Luna Child, and Star Sapphire. Again pretty entertaining.
All can be found here: http://www.pooshlmer.com/touhouwiki/index.php/Comics