Let me get this straight. You want to have multiple themes, one for the blog and one for the e-commerce part of the site? If so, it can be done by using Multisite and once instance of the WordPress software, but two 'sites' or by having two instances of WordPress.
Does the blog exist yet? How does the wp e-commerce exists? Having these questions answered will help determine how you should go about moving WordPress or if you have to. Using the Multisite feature in WordPress 3.0 might be your best bet.
Action and non-action will change your search engine rank in some fashion. Blogs often rank higher because they are updated with newer content more frequently. I'm assuming your websites is going from WordPress software to WordPress software on the home page, so only the content will change and effect your ranks in the search engines.