Hi mqauder,
If you submit your return before the outstanding Payments on Account for that year have become due and been paid, our system will ask you for the 'balancing payment', which is the total amount due for the year, minus the two Payments on Account.
These two Payments on Account will still be due, and will be asked for seperately.
If you would like us to review your statement to confirm that you aren't being charged twice, contact us by webchat or phone here:
Self Assessment: general enquiries
Thank you.