If your program is a program/function within your church, the church will need to be listed as the applicant organization. The application proposal may be for your specific program/project. (Ex. A church that holds its own after-school program or back-pack buddies program)
Your organization may be a separate entity from the church but not have its own 501(c)(3) tax-exempt status, meaning your relationship with the church is what qualifies your organization to receive funding. In this case, the church may be operating as your organization’s fiscal agent, and you would apply under the name of your organization, not the church’s. However, you would also attach a letter from the church that describes the fiscal agent relationship and how long that relationship has been in existence. The letter should also address how funds should be distributed if an award is made. For instance, the letter should note whether a grant check should be made out to the church for the program, or if the check may be made out under the applicant organization’s name.