How to clean up a company's books for the previous years?

I work for a company that purchased QBs online when it was incorporated three years ago, but the bookkeeping was just performed for the first a few months during the first year. After that, there wasn't any bills, expenses or invoices that have been recorded. Now there are more than two thousand downloaded transactions in the Bank account that need to be categorized. Should I start with the most recent year's transactions or should I finish the first year's book first? Do I still bother to enter invoices or bills for the past years? Or should I just categorize the downloaded transactions in Bank? But by doing that, I am recording every transaction on "cash" based accounting, right?