Start by reading this.
http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
Your husband owes 15% self employment tax on the net income (housing allowance AND wages) and you will jointly owe income tax on your combined taxable income after taking your job (if any) and your personal and family deductions, dependents, etc into account. That is likely to be another 15-25%. (The housing allowance is subject to SE tax but not income tax.)
You can reduce his income subject to SE and income tax by deducting work-related expenses like mileage and supplies that are not reimbursed by the church. These expenses can be deducted twice in turbotax, from taxable income and from SE income, but you need to be using Turbotax installed on your own computer to do this, and you need to reduce the deductions according to the Deason rule as explained in the linked PDF.
You can use the Turbotax TaxCaster to estimate the tax you will owe, or you can use form 1040-ES and do it manually.
Once you determine his taxable income and what you owe, you can make the payments electronically at
www.irs.gov/payments. You can use a credit card (and pay a service fee) or have the money debited from a checking account for no service fee. Or, you could increase the withholding from your own job (decrease your allowances and/or specify an additional amount to withhold) to cover the amount owed, if you plan to file married filing jointly.
Here are some other things to read:
