Yes you can enter the invoices with the correct VAT code applied to generate the VAT return and submit via Making Tax Digital, you do not need to use all of the functionalities :)
What VAT code are you using on the invoices?(To look at this you can run a sales by customer detail report form the reports section,select customise in the top right >rows/columns/change columns>tick VAT code and VAT amount>run report>change date range to date range you will be filing for)
As long as you have a VAT Code that is not NO VAT and the date of the invoice or payment falls within the VAT period (depending on if your VAT accounting scheme is standard or cash) then it should populate in the VAT return for that period.
If having looked they are on a code/date range which should show,if you can reply back with a screenshot of VAT 100 report and the taxes page front screen showing the open return,you can add this as an attachment onto the reply or send us a private message on the Community with it and we will look into this further.