If your program is a program/function within your church, the church will need to be listed as the applicant organization. The application proposal must be for your specific program/project. For example, a church that holds its own after-school or back-pack buddies programs.
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 and you must also attach a letter from the church that describes the fiscal agent relationship. The letter should inlcude the length of the fiscal agency relationship and 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 to the applicant organization.