The importance of keeping good financial records cannot be overstated. It's important at tax time; it's important if you want to get financing; it's important if you ever want to monitor your business's progress; it's important if you ever want to sell your business; and it's important if you just want to know where your money is going.
If you intend to keep good financial records, the only way to do it is to develop good recordkeeping habits from the very beginning. In all likelihood, if you start off with bad habits, you'll never get back on track.
Your accountant should be able to advise you on the best way to set up your books. Before you talk to your accountant, however, you may want to learn as much as you can about how to manage your own business finances. A good place to start is with your basic bookkeeping.