1099's are based only on "cash" payments made to you in the calendar year. So when you look at your publisher payment history (second option under ACCOUNTING on your publisher hub page) your 1099 amount should be the total of all check and PayPal payments taken in the calendar year.
1099's are cash-based accounting not accrual-method accounting. Your 1099 total does not relate to your sales and accrued earnings, just the payments. Likewise your 1099 total does not really consider any expenses like print runs or other purchases you made on the marketplace.
For publishers who also receive licensor or freelancer royalties into their customer account, we do attempt to sum together withdrawals you also may have from your customer account with payments from your publisher account, whenever you are using the same tax settings for both customer and publisher payments.