The simplest approach is to make a manual adjustment when you fill in your online Tax Authority VAT Return. In other words, for your first online return, take the eFolioAccounts VAT Report value and supplement it with the pre-registration VAT you wish to claim. This does mean your first VAT Report in eFolioAccounts will not match your actual online VAT return but this is not a problem. You can reflect the pre-registration VAT in eFolio Accounts by entering a Journal transaction to remove the VAT from the appropriate GL accounts and transfer it to the VAT GL account.
For example, if you made purchases of Stationery for 120 (incl 20 VAT) and Advertising for 240 (incl 40 VAT), you would manually adjust the online VAT Return and create a journal entry in eFolioAccounts as follows:
Debit VAT Control 60
Credit Stationery 20
Credit Advertising 40