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Nonprofit organizations tend to have annual fundraising campaigns, punctuated every so often with specific fundraising events that raise money for particular causes or purposes. When you give to an annual fund, you are supporting the general operations and activities of a charity. Ask questions about how the money will be used, and what percentage of it will go to salaries, mortgages, and the like, and how much is directed to programs. Depending on the answer, and depending on what you are most interested in funding, you can talk with the charity about earmarking your gift for specific purposes.
Let's say you want to donate money to go to hurricane relief in Florida, designate that on the check, and send a letter with your donation. Such designations can be attached to material donations. For example, if you have more books than you can store, donating them to a library can be a great option. Depending on the library's needs, they might sell those books to raise money with which to buy new books. If you still want to be able to go and read "your" books, however, you can probably talk with the library about designating those books to be retained.
*When making a designated donation like this, it makes a lot of sense to do some legwork and talk with the charity to which you want to donate first. That way, you'll know the best way for you to help.