Hello all,
Seems I completely missed this very important bit of information on VAT, thank you for bring this up @Hirum.
(I am based in UK and so will definitely get impacted because of this.)
I read above posts and so going to speak a bit below... 
Going through the links, it seems that to get started we should be fine if we use the so called "API-enabled spreadsheets".
The process I currently follow is very similar, where I download all the tax related data from front accounting and then literally copy paste it in to an excel template I have created.
The only exception to above is when I have made journal entries for expenses and vat needs to be reclaimed, for these particular entries I copy paste lines in to above excel sheet, and every quarter the numbers match 100%.
The only new thing I see is that I'll have to use a excel sheet which would communicate with HMRC directly. So some work required.
But in the meantime are there are any VAT users reading this who have developed a way to identify VAT transactions entered using a date from a previously reported VAT period but not included in that periods VAT return, it would be really interesting to hear if anyone has a way to spot late entries to include in the following period. (allowed up to a certain level by UK tax authorities)
Also, does anyone run a "check report" of any kind on their VAT entries. For example if the standard VAT rate is 20% the report would "flag" entries which didn't seem to match that calculation because of user input error.
With regards to the point of late entries or entries which need to be entered in next quarter, I follow a process where I reconcile every bank transaction (80% purchases in my case, and 20% comprises of sales/expense etc). Effectively I check what transaction are pending reconciliation from previous quarter, and they would be included in present quarter.
The template I use has some basic excel formula, which looks up net amount, tax rate from tax report via front accounting, and calculates vat amount on net price, and then check if it matches to what vat amount is in tax report(rounded to two decimal places, for avoiding penny errors).
Hope this long post helps. And please let me know if I can be of any help.
Also, if my memory serves right for zero rate tax, I've found that if you enter tax as zero, it doesn't show it as zero rate, if you don't enter anything it shows as zero rate 
Just found this guys who are already providing solutions it seems
https://www.taxoptimiser.co.uk/Features/MTDVAT
I am sure we'll be fine when the time comes for MTD (Making Tax Digital).
Regards,
GJ