Organization
What I see as the basic design is for a central board of trustees and a charter that makes it easy to set up local chapters where the help is needed or the donations are targeted. The local chapters are where the real work will be done, where people can meet face to face with people who genuinely care, and will take a personal interest.
Donations made directly to the local chapters would require them to give a percentage, say 10%, back up to the central organization. They would then invest some of it in vehicles such as certificates of deposit and treasury bonds, etc. This would be so that enough relatively liquid assets of low investment risk were available to deal with contingencies. This could include funds that are earmarked for specific causes that have not enough accretion of capital to accomplish their goals effectively. The local chapters would only make the specified investments. If they received donations that were earmarked in such a way that they could not be used, those specific funds may be sent up to the central organization to satisfy part or all of the 10% requirement.
The local chapters would be required to make investments that fell into categories established by the charter, or extended by the central board of trustees. Otherwise, they would be required to keep the unused donations as cash deposits, or ask the central organization to hold them until they could be used. If the central organization receives such excess contributions, they may invest them in vehicles that are agreeable to the local chapter that donated the funds. The only objection that should be routinely raised is that the investment has too long of a horizon for maturity. The reason for that is that the central organization should not be forced to liquidate funds at the local chapter's whim, but should be able to offer the funds back upon maturity and reinvest them if the funds are not needed yet.
The central organization should not be directly involved in investments past the indirect financial investments that are prudent. They may, and should, keep cash reserves available to respond to requests from local chapters that they may see from time to time requiring a quick response. Donations made directly to the central organization should be free to be sent down the pipeline to local chapters as the central board of trustees, or their assignees, see the greatest need. Some donations may be earmarked for specific uses, and care must be taken to ensure that such earmarked funds are used for their intended purposes only. If it is discovered that they are not used as intended, a plan to recover those funds must be set in motion. Parameters for such recovery should be set up in the charter, and could be the core of much debate. This is a matter of trust. We need to understand that we may fail, despite our best intentions, to always do right by those who make such earmarked donations. If we do not do enough, there will reasonably be a lack of trust.
Trustees on the central board of trustees should not be able to sit on the board if they are active in a local chapter in any way or anyone reasonably expected to hold any sway over them are currently active in a local chapter. This does not mean they must step completely down, but it should mean that they can be replaced by another active member on the board and may only request to be made active again by the members currently active on the board. This is potentially the most political part of the organization, and careful consideration of the corruptions of this design should be considered and accounted for as best as we can.
Although we have not specified the types of investments that are the core of this project, we have established that they should be in Real Estate and should involve outright ownership of the investment. The specific manner of an investment that is acceptable to be made could be spelled out in the charter, but must be allowed to be extended by the central board of trustees. I will suggest some manner of investments that can be made. I am sure with enough creative minds, other good options might be suggested as well. 
