The bookkeeping account code is asked for to make it easier for you and your accountant to recognize certain incomes and expenses. Your accountant might prefer a certain way of recording the income and expenses but otherwise you might just write CASH, TAX and DEPO (Deposit) in it for example.
If you would like to set default values for the bookkeeping accounts then you can set these by going to Settings > Other options > Invoicing module.
The bookkeeping system is based on the double-entry bookkeeping system which is a set of rules for recording financial information in a financial accounting system. This entry in the Wikipedia explains it more fully: http://en.wikipedia.org/wiki/D