Hello Modern Taxation, 

So QuickBooks online doesn't directly support partial exemption VAT returns. However, you could input the transactions into QuickBooks with the standard VAT codes and then do an adjustment (however we advise that you seek advise from accountant to establish if this method is acceptable) or you can do the calculation outside of QuickBooks using Excel and use the bridging tool on HMRC website to submit the return to HMRC in accordance with MTD.