I’m a church treasurer & can testify that every time we have an event, the money question comes up. It must be either a truly voluntary donation or a reasonable payment for specific materials received (like paying for a lunch)… no stuff like charging for sermons. 
The qualification for NFP is not difficult - most major denominations have established such qualification with IRS. The U.S. headquarters sends a letter (this church is an authorized branch, etc.) to each church for that church’s filing with the IRS. Same letter qualifies with the State. NFP accounting rules are not difficult or really any different from For-Profit institutions. Every dollar must be accounted as to source and use - including donations which are restricted as to usage. Good normal bookkeeping practice suffices; but there is specialized church software which helps.