I got custody of my 12 year son last year when his mum's second marriage broke down, he doesn't get on with my wife and has asked me to choose between him amd my wife and daughter, but he has decided that he would like to go back to his mum's, do I need to go back through the courts again or can I just hand him over if she will have him.

As it is always subject to your local laws, it would be imperative to know where you live in order to address correctly.
You very well may be able to have him start living with her if she will have him back, but it would be importatnt to have the courts consent or at least have it documented that the child/mother are okay with this change.

Msmewithat is right. Depending on your laws, you may or may not be able to just send him over. Either way, even if you can just send him over to her house, it's a good idea to at least keep the courts informed.

I live in West Sussex in the uk.

You will need to inform the courts as to where his legal address is. For the mother's purposes of doing anything legally for him and for any child support to be readjusted correctly.

I don't know what the arrangement is, but hopefully the new change will be a permanent one. Your twelve yo needs stablity.

OK so, not at all asked for, but I am going to through my two cents in just to get it off my chest.
Your son is calling the shots right now and I am not certain this is something that you want to encourage. He has decided at different times that he wants to make a change in his living situation and have you figured out why? I think it would be almost imperative to work through the problem with him and your wife and not allow him to run away. Your not teaching him a very good lesson by allowing him to not face his issues.
That's all. Done preaching.

You really need to take it back to court and get an order.
I would go for an order where the mother would get more or very lenient visitations. Just handing him back to his mom gives him the message that he can manipulate the two of you any time he isn't getting what he wants. Then each time he comes back to live with or visit you he is going to be more demanding and uncontrollable.