Their accountant or finance person needs to get an education, or they need to contract with a payroll service.  There's nothing you can do other than insist that you be paid properly.  Their denomination may have a district office, district treasurer, or other denominational resources who can provide training.

(Whether you are a W-2 employee or a contractor depends on the nature of your working relationship, how much independence you have, and how much control they have.  It's rarely legitimate to choose between the two; you are one or the other based on the nature of the work you will be doing.)

When I was treasurer of my church, I needed to educate myself on how to pay our first staff employee -- it requires a fair amount of detail oriented work to learn and follow all the state and federal regulations, and there is no way I can provide that kind of training here.