Your employer deducts a payment from your salary before they then work out how much tax you need to pay. This gives you tax relief on your payment at the basic rate of tax, 20%. If you already receive basic rate tax relief on your pension payments (PPR), you would enter the gross figure in the payments to registered pension schemes, as this will allow you to obtain a further 20% tax relief, by extending the threshold at which you become subject to higher rate tax.
If you enter the gross figure in the other box, you are declaring that you have full relief still to claim. You can see the guidance on completing SA100, under the section tax reliefs here:
How to fill in your tax return (2022) Updated 6 April 2022