Should I use General Method for calculating taxable portion of 1099-R if different from gross distribution because I have a clergy housing allowance?

I'm retired clergy.  My 1099-R has my gross distribution which includes my housing allowance in box 1. Box 2b, taxable amount not determined, is checked. I calculated the taxable amount by subtracting our housing expenses from the gross and entered that in 2a. As I proceed in the Step by step, it sees that 2a doesn't match 1, and asks if I am using the simplified method or general method to calculate the taxable amount. which should I choose?