Self-employment tax is part of your overall tax liability on Form 1040. Estimated taxes are paid with Form 1040-ES (or, if paid online, are paid as if you had submitted Form 1040-ES) and no part of your estimated taxes paid applies specifically to self-employment tax, they apply to your overall tax liability. There is no way to make a payment that is specifically allocated to self-employment tax (even though you might have determined the necessary payment by considering only self-employment tax, say, because your income is low enough to otherwise be nontaxable).
