To avoid duplicates between Freshbooks or Harvest and GoDaddy Bookkeeping we usually recommend you import from either your main bank/credit card or the eCommerce provider. There is no duplicate transaction filter in GoDaddy Bookkeeping, so if your numbers don't look right, it's probably because you're having some duplicate Income items show up. Most of the time we find Freshbooks or Harvest to be most useful for our customers whose banks cannot get connected to GoDaddy Bookkeeping.
Which of the two is better to keep? In general, we recommend importing from the bank account only, that way the maximum business deductions can still be captured. GoDaddy Bookkeeping works best as a cash-based accounting system, which can help you track your income as you have the liquid cash flow.
If you prefer to keep both your Freshbooks or Harvest account and bank account linked to GoDaddy Bookkeeping, you're best off to continually monitor your ledger and delete any duplicates that show up. You can also re-categorize your bank deposits as "HIDE(duplicate wrong income)" so they will not affect your income.