For some time now, I've been trying to find a novel I've read sometime in the early 2000s. At long last, I gave up and will try asking for your help.
All of the details I write below are from my muddled memory and may be false or misshapen.
First of all, I think this is a series of novels, and not just one.
In this world, the characters can gain (magical) powers by having special stones imbued in their backs when they are children. The two main characters are brother and sister and each has an abnormal amount of stones in their back, something like 7 each. The stones are colourless before being placed in one's back, but then change into a colour of the person's power.
The main characters' home is destroyed and they must travel. In their travels they see the magical stones' miners and their children who mostly become miners themselves, as their stones turn to mud brown, the color of the earth in which the stones are found. The characters witness the ceremony performed by an individual wrapped in many scarfs, without a stone on their back.
The end of one of the novels ends with events concerning a prison in a parallel dimension/world. The characters travel to and from the world trying to break someone out of the prison.
The novels I read were probably in Croatian, but if so, that was probably a translation from an English original. Decided to mention it in case I'm mistaken and there is no English translation.