We're using direct integration which works fine for the customer and they are correctly redirected to the 3D secure page for validation and enter the password if required by the backend. We want to take payment over the phone as well. Sage Pay offers terminal transaction within My Sage Pay page, but I couldn't see to find any documents that we can do same but from our backend. http://www.sagepay.co.uk/support/15/37/process-a-terminal-transaction
It's exactly the same as your ecommerce integration - all you need to do differently is specify AccountType=M in the transaction post. This will suppress 3D Secure checking. You will need a MOTO MID on your sagepay account, though.