I understand that SEP IRA contributions for self employed are based on ~19% of net profit. However, one does not know net profit till after filling your taxes. So if I contribute money in 2013 to SEP IRA, how does IRS know if it applies to
If you're a sole proprietor, the IRS only knows the intended year of contribution because of the amounts claimed on your 1040s, as an above-the-line deduction. The IRA custodian will code the fact that you made a deposit, but will not code it for a tax year. The employer does need to track this though, and the IRA custodian may have a contribution remittance form where you list it.
In practice most sole-pros seem to do their SEP deposits at the time of tax filing, for the reason you mention - you don't know your net income until then.
-Tad
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