MTD is the new scheme brought in by HMRC, effective 1st April 2019. This means that VAT returns must be submitted through the new MTD scheme (which QuickFile supports) unless a business is exempt. Eventually more aspects of tax will be made digital too.
You would first need to enrol on MTD before you can use it. What @FaradayKeynes mentions above relates to this. The VAT process in QuickFile is almost identical to the service we used to offer prior to MTD. But if your agent is submitting the VAT return on your behalf, they would need an Affinity account and link it with yours to do so.
These posts may be of interest: