Submitting directly via accounting software
For my own VAT return I opted to submit directly using a well known accounting software package as it promises me that MTD is as easy as ABC. VATNAV is in its first week of business and so is by no means using MTD on a compulsory basis yet, but I thought I should throw myself in at the deep end.
Being a novice to accounting software I wanted MTD to be as easy as possible for me, and as a business with no particular VAT complexity, there is no reason why accounting software wouldn't work. Once I logged into the VAT section of the system, it asked for my VAT number and VAT quarter end date, and for permission to connect with HMRC. This was really easy to do and, having already registered with HMRC earlier that month, the two systems instantly set themselves up and started to "talk" to each other. The only issue here was that, in my case, they seemed to be speaking different languages...
The issue I faced arose from the fact that I have only just registered for VAT. Most business' date of registration for VAT is not the first day of its quarter. Mine was mid quarter - let's say it was 3 June. HMRC had communicated to my accounting software that it wanted a return for 3 June to 31 July, and my software decided to also demand a return for the period 3 May to 2 June. It said that this "fake" return had already been submitted but I needed to mark it as filed. This was clearly a glitch in the system, but it meant I needed to clarify what was going on. This was 5 August (I'm on a July quarter) and given the proximity to the June deadline, there was a 25 minute wait to speak to my accounting software team, and HMRC put me on hold for half an hour before hanging up. I decided to wait until 9 August to give everyone time to recover, and it was pretty easy to get hold of people on the phone then.
Solving the issue was a bit long-winded, because neither HMRC nor the software helpline knew anything about this, and didn't know what would happen if I marked it as filed. Eventually, I decided to click "mark as filed" anyway, and this seemed to get the system back to normal. I waited four working days to phone HMRC to check that nothing had actually been submitted for the fake return. Nothing had. Great! My accounting system was showing the completely wrong information due to the "filing" of the fake return, so I added all the pre-3 June information via the "adjustments" section. (All MTD-compliant system should have this section but I would advise using this in exceptional circumstances only because feedback from others have said it can impact the figures within the system itself).
Anyway, once the system got back on track, submission was really straightforward and I had a receipt emailed to me automatically. I guess the moral if the story here is for your first MTD return, allow yourself plenty of time for any glitches/delays etc...I am very glad I started submitting my return 5 weeks before my deadline!!