Fresh Store Builder is a standalone script that comes with everything you need to building amazon affiliate websites.
FSB does not work inside of wordpress, it works side by side with WP.If you have wordpress installed on your main domain then you can install FSB in a sub-folder (Guide http://guides.freshstoreinstant.com/fresh-store-builder/common-problems/how-to-install-fsb-in-a-sub-folder )
If you want Fresh Store Builder on your main domain then you must delete wordpress. You can then upload wordpress in a sub-folder called blog or whatever you want. Then when you visit yourdomain.com/blog/ it will load up wordpress.FSB and WP have no connections.
We do offer the Fresh Booster Plugin which helps connects a WP blog and FSB store.
The Fresh Booster Plugin will let you embed products from your store into your blog post/pages and widgets. (This guide goes over what the Fresh Booster Plugin does http://guides.freshstoreinstant.com/fresh-wordpress/fresh-store-builder-and-wordpress/how-to-install-fresh-store-booster-wp-plugin )
You don't need the Fresh Booster Plugin to make the WP/FSB combo work but it does help. Without the plugin you can still manually add links from the blog to fsb and back to the blog using content, banners or just navigation links.