Can I reduce my quarterly estimated tax payments by the amount of tax I estimate I will owe after taking the 25% SEP deduction?

@amyb5984 - yes, you are under no obligation to adhere to the 1040 ES vouchers that TT generated.  If you have a better estimate (up or down), you can use that. 

Be careful, though.  If you are referring to the self-employed retirement deduction for a SEP contribution, the maximum permissible SEP contribution is 20% of net earnings.  Net earnings are net profit minus the deductible portion of self-employment taxes.  Mistakenly calculating based on only 75% of self-employment income being included in taxable income could result in underpayment of your estimated taxes.