You do enter amounts in both boxes typically. The first box you enter the housing allowance you actually received. This will be added to your income on form 1040, line 1h as other income "excess housing allowance." That is, at that point, taxable income. In the second box you enter your actual expenses for housing. This will remove the income from taxable income lines (1h).
Next, the housing allowance and your clergy wages are subject to self-employment taxes and are added to the Schedule SE. You will be asked questions to determine the self-employment taxes due. For example, if you have an approved form 4361 or if social security and medicare have already been withheld. The answer to those questions may remove amounts from the Schedule SE as applicable.
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