Lily,
If I understand the situation correctly, this amount is paid to the pastor once a month and varies each time. Does the church do any witholdings for the pastor? Some churches do no withhldings at all and the pastor still receives a W2 but pays all his taxes as self employed.
If the church doesn't do any withholding, you have nothing to do. Just add the amount once a month to his checks and you are done.
If the church withholds taxes for him it get a little trickier. I am assuming that when you say changing him to weekly you are talking about under the employee setup as to how many checks they get a year. I wouldn't change this. Here is how the program calculates taxes. Say the pastor makes 1,000 gross per pay check. The program is going to take the 1,000 and multiple it by the number of pay periods in the year. So biweekly would be 26 checks a year, that calculates to 26,000. It then figures the tax on 26,000 according to the tax table and then divides the tax by 26 to come to the amount for the individual check.
If you change the pastor to weekly and add the bonus, say for example the bonus was 250 making the gross 1250. The calculation would be 52 * 1250 = 65,000. It would then calculate the tax on 65,000 and divide it by 52 to come up with the tax amount for that check.
So all of that said. Normal practise when adding a bonus to a check is to just let the program calculate the taxes under their normal checks per year. This might result in more taxes than necessary being taken out of their check. Here is a blog post I found from someone complaining about this problem.
http://thematurationofshane.wordpress.com/2008/03/10/
You do have another option. According to PUB 15 (Circular E) you can choose to withhold a flat 25% of the bonus from a paycheck. See page 14 of the 2008 Pub 15.
http://www.irs.gov/pub/irs-pdf/p15.pdf. If you are withholding Social Security and Medicare you will still need to withhold those amounts from his check as well. The 25% is federal income tax only. You will also want to check to see what your state wants to do.
Neil is right all of this is going to be reported on the W2. I have just been talking about the tax caculations.