As a VAT registered business you will need to enable the VAT settings to ensure Clever Accounts is correctly set up. Furthermore, you will need to elect which VAT scheme you wish to proceed with. The choices are "Cash Accounting" and "Standard Invoice Accounting". The major difference between the two being the way VAT is declared.
Briefly, on Cash Accounting, VAT is declared based upon payments you make and payments you receive. Whereas on Standard Accounting, you declare VAT based upon the invoices you receive and the invoices you send customers. This basically means that you could end up paying VAT on an invoices you have yet to receive payment for!
Unfortunately, it's not that straight forward and there are various restrictions for both schemes, so it is always beneficial to consult and accountant.