Would I be right to assume you deposited the money into the business bank account from your own?
If this is the case, your current account on QuickFile should have the £1000 as “Money In”. Just tag this transaction as a transfer from the Directors Loan Account (DLA), and that’s it!
This leaves the DLA as “£1000 overdrawn”, which shows the business owes you the money, and leaves the current account with a balance of £1000.