"religious" non-profits operate differently than regular non-profits per IRS laws. The WTS audits itself, has a department for that alone.
http://nonprofit.about.com/od/faqsthebasics/f/What-Is-A-Faith-Based-Nonprofit.htm
There are no direct legal benefits associated with being identified as an FBO. However, there are benefits and drawbacks associated with being a certain type of FBO. For example, churches that meet the requirements of Section 501(c)(3) of the Internal Revenue Code can claim tax-exemption without a determination from the Internal Revenue Service (IRS) and have special protections that limit how and when the IRS may audit them. Additionally, certain religious organizations, including churches, are exempt from filing IRS Form 990 and may be exempt from filing state information returns and charitable solicitation registrations.
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Nonprofit corporations must not distribute profits to members, officers or directors. A nonprofit corporation cannot be organized to financially benefit its members, officers or directors. However, reasonable salaries and expense reimbursements are permitted. Read more: http://articles.bplans.com/small-business-legal-issues/running-your-nonprofit-corporation/192#ixzz2bFKoxwrm
When a nonprofit corporation dissolves, its assets must be distributed to another tax-exempt group. Since tax-exempt organizations and their assets cannot be owned, they can never be sold. If the directors of a nonprofit decide to disband the organization, they must donate its assets to another nonprofit group. This also means that once property goes into a nonprofit corporation, it cannot later be distributed to a member or director. Read more: http://articles.bplans.com/small-business-legal-issues/running-your-nonprofit-corporation/192#ixzz2bFL5KZBX
Organizational structure of nonprofit corporations
Like any corporation, a nonprofit has a board of directors to make important policy decisions, officers (president, treasurer and secretary) to oversee and manage the day-to-day operations of the organization, and possibly employees to do the work.
Unlike regular corporations, however, nonprofit corporations do not have shareholders or owners. (Nonprofits are owned by no one person or group of persons and cannot be sold. In the event the directors of a nonprofit want to dissolve the corporation, they must distribute all of its assets to another nonprofit corporation.)
Read more: http://articles.bplans.com/small-business-legal-issues/running-your-nonprofit-corporation/192#ixzz2bFLJaNVr