I would think that they might be entered as a Bank transaction. Click on 'Bank' on the left hand side of the home screen and depending on whether you are entering them as Bank Account or Cash Account, click View/Add. Then 'add the transaction' using the nominal code for sales. If the client is VAT registered, don't forget to enter the amount including VAT and it will then deduct the VAT for your VAT Return.
I'm not surprised you have found it confusing as I had the same issue when I first started using it. Hope this resolves the issue.