Sorry, maybe that was badly explained.
If, for instance, your earnings are £15,000 for the tax year including your mat leave / SMP payments, and you have the full 39 weeks' SMP in that time, they will deduct £3900 from the £15000, giving you earnings of £11,100 for that year instead. Which means that if you do qualify for tax credits, you'll get more for that year.
I'm £11,000 down on 2012-2013, but with the £3,900, the figure they use is £14,900 less than 2012-2013.
If you know how much your salary will be down for the year, wait until you have your award and call them up, giving the accurate figures for this tax year. Otherwise, it's all based on the previous tax year's figures.
Clear as mud?! :-/