VAT payments should only be recorded in the "New Tax Payment" screen if you are recording the payment you made for a VAT return that was not processed by Crunch or if your accountant has given you specific instruction to do so.
All of the VAT returns that were processed by Crunch will appear in the "VAT returns" subtab, under the "Tax" tab, and the related payments should be recorded from that list as follows:
In order to pay a VAT return, it must already have been filed by Crunch. Once the filing process is complete you will see a date in the "Date filed" column, and you will be able to click "Record VAT payment" in the relevant return's "Options" menu.
In the "Record VAT payment" screen, fill in the details of the payment (the full amount of the VAT return is pre-entered).
Clicking "Record VAT Payment" completes the process, causing the payment to appear in the "Tax payments" list too.