Let me start off with some things not to do from experience:

1. Do not place mass quantities of banners on the main page of your site. For the most part surfers do not pay attention to banner ads.

2. Do not sign up with affiliate programs that have nothing to do with the content or scope of your website.

3. Do not put all your faith in one affiliate program, you should have a few backups just in case.

4. If you do place a banner or two on your main page don't pick the super flashy banner that makes your eyes hurt.

Here are a few things you might want to to do:

1. Pick affiliate programs that are well recognized by the general public.

2. If you must place a banner or two on your main page try and locate a banner that matches the color scheme of your site.

3. Use text links in the main content of your site (instead of banners) to funnel your visitors to your chosen affiliates.

4. Pick affiliates that match your content fairly close but try to avoid affiliates that would create competition for your site.

5. If you are showcasing multiple affiliate programs make sure you make navigation to your affiliates fairly easy for your visitors.

Like I mentioned before I don't claim to know it all when it comes to using affiliates. All I wanted to do is give a bit of information that I have gained through trial and error in hopes that what I know can be used.