If you are an employee of your church and unless you own a business where you are doing "admin" work for several different churches...you are most probably an "employee" of your church...so ... your compensation must be reported on a W-2.
1099-MISC are for reporting independent contractor payments. That form is only appropriate for payments in situations like I mentioned above (doing admin work for multiple churches)...or maybe a landscaper that takes care of multiple business properties.
BUT ...if you have not been withholding payroll taxes, matching FICA, and filing quarterly 941s...you have a problem.
PLEASE contact a knowledgeable CPA or tax professional that will be help you with the back payroll taxes and filings.