I am an accountant, and from time to time a certain Jewish org that does charitable work asks me to do some work for them. I feel like I need to do it, can I pay myself with maaser money for the work I do for them?
For the work that you are going to do, you may surely do it. Regarding past work it may also be done. Please see the following post https://dinonline.org/2017/09/13/deducting-from-maaser-money-owed-by-yeshiva/
Rema Y:D 257-5, Shach ibid 12.