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What steps do I follow when we owe money to a client and they owe us, and they have paid their account less the money we owed them?

If you receive their payment into undeposited funds, then do a 'Pay Bills' transaction and select undeposited funds as the account the money is coming out of, they will balance each other out. 

You can then go into 'Prepare Bank Deposit' and create a nil deposit by ticking both entries.  (They will show one as a positive and one as a negative - assuming they are the same amount?)

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