Both pre-processing (processing the sounds and then working with them), and post-processing (working with the sounds and then processing them) are acceptable - there are no rules. Both will create subtley different effects, and it's up to you to decide which is best... it will vary wildly from one sound to another and there is no "right" answer.

It's not the most useful answer in the world, I know, but just experiment. It might take you longer than someone telling you what to do, but you'll come up with something inifinitely more original just whacking on random effects (even if you don't know what they do or how they work) and playing until you get a good noise.

You'll feel much more pride afterwards too.