This is a very complex question and in order to create such an arrangement you really should work closely with both a CPA and an attorney. There are several things that need to be considered, such as what type of entities are involved, what industries, and how they should be structured. This includes all of the tax considerations for the owners/members/shareholders of each entity as well as taxation of the businesses. The most important issue, however, is that if you want a parent company to be the owner of a not for profit business, the parent company cannot be a for profit business. There are ways to structure your businesses so that a for profit is associated with the non profit.
In general, to set up a parent company, you would first establish that company, be it an LLC, or traditional corporation and determine how it will be taxed, partnership, s-corp, c-corp, non profit. Then you would set up the additional companies and indicate that they are wholly owned by the parent company. Each of the subsidiary companies would report their income and expenses under the parent company. But again, this is really a discussion that needs to be had face to face with an attorney and CPA.
