I am self employed filing as an s corporation with w2 to myself; I paid estimated tax but how do i pay self employment tax

With an S Corporation, the flow-through amount shown on the Sch K-1 is NOT subject to SE tax. 

You do report the amounts from the Sch K-1 on your F1040 and pay income tax on that.

The amount shown on the W-2 is also reported on your F1040 and you pay income tax on that.

Thus on your F1040, you report and pay income tax on the amounts from both the W-2 AND the Sch K-1. 

FICA should have been withheld and the S Corporation should have filed F941 and paid the FICA and any federal income tax withholding to the Treasury Dept via the forms 941.

I don't quite understand what you mean by the estimated tax?

Normally estimated taxes are paid via F1040ES.  Those are filed quarterly, and usually filed to pay income tax for sources of income that do not have withholding....such as the income shown on the Sch K-1.

Through the use of your withholding on the W-2, if you estimate carefully, you could have enough withheld through the W-2 so that you wouldn't have to file/pay F1040ES.

But that only works if you pay a large enough wage on the W-2 and you probably have to claim extra withholding.

It all depends on the the relationship between how much income is shown on the Sch K-1 and the amount of wages paid to you on the W-2.