Autopay will not be affected, it will always draw what is outstanding for you bill. It won't draw anything additional.
These will be the outcome depending on the amount set.
Full amount - In the event the amount due is the full amount, this will proceed as normal. If you Top-up your account before the repayment completes, the repayment amount will be credited to your account, and any over payments will be credited to your top up.
Fixed amount - This will still look to go ahead as normal, and the amount set will be debited as normal.
Minimum amount - This will still go ahead as normal.