Self employed individuals make estimated tax payments quarterly to the IRS because there are no taxes withheld on that income. If you are having additional taxes withheld on your W2 income to offset the self employment and federal income tax he will owe on his return, the only issue would be to make sure you have had enough withheld. If you choose to have your withholding increased, instead of him making quarterly estimates there would be no need for him to submit quarterly payments. The IRS doesn't care where the taxes are withheld as long as you are, in fact, getting them submitted.
