Hello ibrahimwhithornt, thanks for posting on the Community.
When submitting VAT using our bridging tool, HMRC will only receive the figures on the spreadsheet (and not those which show on your VAT 100 return in QuickBooks for one company).
This means when submitting group VAT, you'd combine the figures on the spreadsheet, so that you're submitting the total for both companies.
You can then mark as filed the return for company 1 and company 2 in QuickBooks after filing.