Philip Bump posted a guide for The Atlantic Wire on how to use encryption to hide your activity from the NSA. Except it’s a pretty shit guide. Instead Micah Lee has a great guide for the Freedom of the Press Foundation and Tactical Tech has another nice outline with guides for good secure software usage.
The latter two guides are far better than the first, but the gist of all of them (and as I have said before) is that truly secure communications is hard, cumbersome, and requires both parties to be using it. That latter is the hardest obstacle to overcome.