Your post is a little jumbled so forgive me if I have missed anything important
If you have signed to say that you will repay training fees if you depart the company within a certain time then yes they can take the money from anything they owe you. I presume this is what you mean by the repayment scheme.
I would not try to be clever on the 'common law' issue - simply ask for a conversation about how much is owed (if you dont believe it is the full amount) and how it will be repaid.
I also dont think that being asked to sign the agreement before you started the course (even if it was at very short notice) can be called duress.
My advice - have a sensible conversation with your employer sooner rather than later and come to an amicable agreement.
© 2010 Reed Business Information Ltd.