Any payments made to your top-up account will be used to first repay any outstanding balance on your card. The remaining funds, this will be credited to your top-up account.
e.g. If you have an outstanding balance of £200, with a credit limit of £500 this would mean you have an available limit of £300.
If £400 is paid into the account this pays off the £200 credit used and the additional £200 goes into your top-up account.