This is the same as any case where income is variable. How do you deal with the months where expected cash flows are lower than projected?
When I got married, my wife was in the habit of allocating money to be spent in the current month from income accrued during the previous month. This is slightly complicated because we account for taxes (and benefit expenses) withheld in the current months' paychecks as current expenses, but we allocate the gross income from that check to the following month for spending.
The benefit of spending only money made during the previous month is that income shocks are less shocking. I was working for a start-up and they missed payroll that normally arrived on the first of the month. Most of my co-workers were calling the bank in a panic to avoid over-draft fees with their mortgage payments, but my mortgage payment was already covered. Similarly, when the same start-up had a reduction in force on the first day of a new quarter, I didn't have to pull any money from savings during the 3 weeks I was unemployed.
In the end, you're going to have to allocate money to the budget based on the actual income--which is lower than your expectations. What part of the budget should fairly be reduced is a question you and your wife will have to figure out.