Witches are magical creatures of the magic dimension and are the magical opposite of Fairies (one side being positive and the other side being negative). Because two sides are plus and minus, as the the old word aptly says: "Opposites attract each other", Even though they are magical opposites, witches can converge their magic with fairies.
Witches and wizards are similar in appearance to humans and Fairies. However the source of their magical powers is from their negative feelings and from darkness, while that of the Fairies is from their good feelings and from light. This reflects itself in the dark clothing, punk-like and gothic-like of the Witches.
Even if some witches have used their powers for evil purposes, most witches are not necessarily evil as has been mentioned several times in the series, examples being Miss Griffin who helped the Company of Light fight the Ancestral Witches (as an effort at redemption for having initially worked with the Ancestresses and Valtor, though it was mentioned by Valtor that Griffin and Faragonda were already friends when Griffin was still with the Ancestresses when he says that Griffin left the Ancestresses to side with her "great friend" Faragonda), Miss Faragonda (who was a Witch but later became a Fairy), Mirta, Lucy and the many other Witches of Cloud Tower who helped the Fairies against the Trix, Lord Darkar (unsuccessfully due to their rivalry with the Fairies) and Valtor many times.
Lucy once even told Mirta that not all witches were evil like the Trix, and that some are strong and proud, like Miss Griffin, whom she considered as a role model.
In the Shaab Stone arc of the Winx Club Comic Series, Miss Griffin says that both witches and fairies fight evil, but while fairies use good magic, witches use bad/dark magic (witchcraft).
Like their counterparts witches must attend school to become full-fledged witches and practice their craft. Most witches attend the Cloud Tower School for Witches in the Dimension of Magix. At school, Witches are taught and trained to increase their powers and to use their powers responsibly (Yes. Witches do value responsible and moral usage of their powers) as to help preserve the Magic Dimension and fight against evil, even though it is by using dark magic.
Witches prefer working alone, especially because witches have tendency to betray each other. But there have been exceptions, such as Trix and Ancestral Witches, who have always been 'supporting and faithful' towards each other within their respective groups in loving (albeit very warped) way: even if there are sometimes rivalries between group members.