You should be able to enter what you've already paid the tax return I'd have thought
In the Employment section I had
'Pay from this employment – the total from your P45 or P60 – before tax was taken off'
'UK tax taken off pay in box 1' (i.e. above figure)
I corrected the 'Pay from this employment' bit and the correct figure was used in the calculation at the end. I'd think your additional PAYE contributions would/should be included in the 'UK tax taken off pay in box 1' bit?
So it wasn't that I submitted it and then later was told I'd overpaid, the provisional overpayment was calculated on the basis of what I was about to submit.
If that makes sense.
(I am most definitely not qualified to offer advice)