First, your church needs a Federal Employer Identification Number (EIN). This is the business version of a Social Security number.
Not sure if your church HAS an EIN? Look on the W-2 -- it will be there. No W-2s? Call 1-800-829-4933 to find out. (I recommend you get a book and a cup of coffee or tea, as you're likely to be on hold for a while waiting your turn).
If you don't have one, you'll need to get one. To apply for a FEIN, go here. This is the first step to be able to give your pastor a W-2, or give contractors a 1099.
Once you have your EIN, you'll need to register to do the W-2 and W-3 online. You register with the Social Security Administration's Business Services Online (BSO). BE SURE to safely note your login and password.
You'll likely only use this website once a year, and it's easy to lose track of the login information.
Once you have your EIN and a login at the BSO site, you're ready to complete the W-2.
That's pretty much it, if the pastor is your only employee. The IRS says if the pastor is your only employee, and you are not withholding taxes, you do not need to worry about filing quarterly 941s.
The pastor's compensation form from Charge Conference provides little notes on the far right column to tell you where each item goes on the W-2.