bernie007: it seems they have no intention of helping, only will take anything that goes in the account.
This is "set off" at work. More info here....
http://www.financial-ombudsman.org.uk/publications/ombudsman-news/40/40.pdf
The first thing to do is to open a basic bank account at another bank and transfer as much of your banking to it. If Halifax have already withdrawn your £3000 there is nothing to stop you transferring your wages as well.
Read the article and make sure Halifax have complied with what little small print there is about this practice.
For others reading this what are the lessons? Don't save with an organisation you are or could be in debt with. Try to have a credit card from an organisation you have no other banking arrangements with.
Recognise that an overdraft (unlike a loan) is repayable on demand. In particular it is very difficult to move wages from an account in overdraft because the likely consequence is withdrawal of the overdraft. Get any savings out first.