There's two options for this situation.
As you already have the payments recorded in QuickBooks from Sage, you don't need to record the payments against the filing as this will cause a duplicate. Its fine to leave this showing as filed with 'record payment' on the taxes screen, HMRC don't see this part of QuickBooks, but I understand this doesn't look as 'tidy' as having them all marked as paid.
If you choose to mark them as paid, you'll need to locate the payments from Sage by viewing the Chart of accounts in QuickBooks and locating the account that the payments were posting to. After finding the two payments, delete and then go to the taxes tab and record the payment against the filing. The recorded payment will post to the payment account selected and as a debit against the VAT Suspense account.