From what you have described thus far, I think you are over complicating matters no matter what the regime is.
In the most basic of formats, you would need to have one control account for VAT which will receive transactions for both input and output tax. For example, with a 20% VAT rate a sale amounting to 120 of whatever currency will reflect 100 Dr to the Sales account and 20 to the single VAT control account. A purchase of 60 will generate a 50 Cr to the purchases account and 10 Dr to the single VAT control account and if they were the only two transactions, your VAT liability will be 10. If you are required to pay the 10 over then the accounting will be Dr Bank, Cr VAT control leaving the VAT control account at 0.
However, things aren't always that simple as in the meantime, there may be further transactions outside of the VAT ¼ being settled where the debits and credits will continue to accumulate so it may be unlikely that the account will ever stand at zero but your VAT database in the software will assist in reconciling your VAT return.
At the next ¼ return of course, transactions which have occurred in the meantime will be accumulated giving you the data you require to complete your next return and so it will continue.
If you jurisdiction is the United Kingdom (HMRC) there are different VAT regimes for different business styles.
This GNU reference referring to HMRC explains more as follows: