YA Fantasy. A hardback book I owned as a child that was part written and part comic, I believe it was aimed at teens, and it was fantasy.

[Cameron-Jade Ashman]

The main character was a human teenage girl with short (shoulder-legnth?) dark hair. She got transported to another world (I'm pretty sure it was a world that she had been to before, as it was implied that this book was not the first of a series from what I remember) which seemed to be set in a forest. In this world there was a boy made of wax, the top of his head like I candle, and I think his 'skin' was blue. I remember him being plump and wearing what looked like some kind of school uniform that was too tight. I'm pretty sure he wore a tie. There was also a girl made of wood like a marionette. I don't remember enough to describe her physically, but I think I remember her being somewhat superficial. I think there was also an older male character, like the adult who knew why the girl had been brought back, but I don't remember anything about him. I'm pretty sure that the main character was told that she was brought back because the alternate world was at threat by some kind of bad guy, and she was supposed to stop him. She might have had fire powers, but I'm not sure; I just vaguely remember seeing her with orange glowing orbs in her eyes; perhaps from using fire powers, having a vision, or even some sort of hypnosis. I also remember her being manipulated into having false memories of/thinking that she's talking to a loved one (her mum?) by the bad guy, so maybe this is why I remember seeing glowing in her eyes.

This book definitely came out before 2013, but I'm not sure what point between 2000 and then. My guess would be some time after 2007. The way the main character is drawn (from memory) reminds me of how Liz looks in the animated Hellboy films; full lips, rounded nose, bold eyes without being necessarily detailed. I think that the book was American, but my nan bought it for me in England.

[Becca]

This sounds like the Abadazad series by J.M. De Matteis and Mike Ploog. The first book is The Road to Inconceivable, the second is The Dream Thief and the third is The Puppet, the Professor, and the Prophet. The wax character is called Mr Wix, and the puppet / marionette girl is Mary Annette.

[Kris]

This copy of The Road to Inconceivable by J.M. DeMatteis (Becca's suggestion) on eBay shows some inside illustrations:
https://www.ebay.com/itm/226532095349