Business Expenses through payroll

Chris - why don't you ask your accountant now, and why isn't s/he showing you how to use the software?

Not 100% sure how you've made this work in the past but with CB you process your payroll, as payroll, and that fits the salary & PAYE figures into the bookkeeping and you use the Purchase>Expenses function to claim expenses that you've paid out on behalf of the business.

Dividends are created as debts to the shareholder(s) via the Tools>Dividend tool and you can chose how to pay that off, ie from the bank account or director's loan account.

Getting the bank transactions into the books is best done directly from bank feeds via Yodlee or by downloading your statements from internet banking and then uploading them to CB, this way, in theory, you bank can never be out as it's replicating what's in the actual bank account.

Sorry if that's a bit long winded but I wasn't sure what bit you weren't using or understanding.