Step 1: get the statement in a usable form
Do this within the first week of the following month. The details are still fresh, staff remember what an odd transfer was for, and errors can be fixed before they reach the VAT return or the management accounts.
Download the month’s statement for each account from online banking. Excel or CSV is easiest to work with; PDF is fine if your software can read it. Check that the opening balance matches last month’s closing balance on the statement, and that you have every account, including USD accounts, deposit accounts and credit cards.