NGOs are much more simplistic than prior games. Basically, you will start out with a set amount of money, which you may invest in any country or countries of your choosing. Depending on how much influence you have in the country, you will receive a portion of its income (much as a player would).
For example, say a country has 900 influence invested in it by several major powers. You put in 100. You now have 1/10 of the influence in that nation, and so will receive 1/10 of its client income each turn.
While NGOs have fewer resources, they are also invisible and have fewer fields to manage. If you're one for sowing chaos, controlling stuff from behind the scenes, etc. they are definitely the way to go.
If you prefer nations, of course, you got in before the closing of signups, so I'd allow you to change your mind.