Yes, you can upload your own spreadsheet with your VAT return calculation. You will need to have the 9 boxes required by HMRC with the final numbers on your spreadsheet on a single tab.
You can link the numbers from anywhere in your spreadsheet to the 9 boxes. Once you’ve uploaded the spreadsheet you can adjust the respective cell references for the 9 boxes to your spreadsheet layout.
Here is a step by step video guide on how to upload and file your spreadsheet VAT return: