If you aren't experienced with affiliate programs and the SEO implications then you are probably going to find trouble. You can do affiliate and still have a strong site in the serps but you need to properly manage the process.
A common mistake is giving your affiliates sites a copy of your site content. This will lead to duplicate content issues.
Another mistake is accepting everyone into your program. This can lead to some affiliates who may do some very high risk moves that can risk your site and/or brand.
Also you probably will not want to allow affiliates to register domain names that include your brand or company name. This could lead to consumer confusion and some webmasters linking to your affiliates when they think they are linking to your main site.