If you are making this kind of question then it is 100% clear that you are not quite understand how the whole thing works. Let me give you a very general outline to help you make it clear in your mind (and start researching).
- you have something to promote (whatever) in this case an affiliate site
- you have to get traffic on this promotion, this can be done in many ways. One of them is organic (google search).
- I assume you go with this method. Then you got to find the "right" keywords for the product you promote and start building your ranking with those keywords.
- In this task there are many programs (like senukex and many others) to help you rank your keywords.
* my suggestion is that you start without any programs until you have a clear vision of what you have, then what you need and how to get there.
cheers