I believe you're thinking of James Celemen's Wit'ch Fire.
Someone else asked a similar question "Girl with bloodstained hand after hitting her menstrual cycle-fantasy-dark magic":
am looking for the series that begins with a young girl who suddenly is reaching for an apple, then it shrives in her hand and she looks and it suddenly is turned red up to her forarm. [sic]
And elsewhere someone asked, "Name of Book about a young witch with a Red Hand":
I've been searching for a book series (I know there were 3 of em). What I remember is a young witch with a red hand that faded everytime she used magic, a one armed gaurdian or juggler who helped her and about a demonic entity she was fighting.... part of the book she had to fight a evil being who had thousands of little spiders in her womb. I know it may sound like a crazy book series, but any help would be appreciated.
I can't find anything about her other hand becoming red, but a lot of the other information ties to it.
Thirteen-year-old Elena is the daughter of kindly orchard keepers who have no idea their little girl is the reincarnated sorceress Sisa'kofa, "wit'ch of spirit and stone," dead for more than five centuries and now the world's last hope for defeating the dreaded Dark One and his minions.
For the record, this planned trilogy is now actually 5 books.