Here are some things to consider with SEO when moving from one e-commerce platform to another.
1). Ultimate Cart is much more SEO friendly than Site Builder. You have much more control over the URL structures and URLs themselves. You can customize just about anything with that regard. There is much more room for SEO customization with Ultimate as opposed to Site Builder.
2) Shoppe Pro can transfer over your categories and products from site builder as far as the product info, and Meta title, meta description, keywords etc direct from your old site builder automatically. (You need to request this free service at the link on the bottom of this page). Those Meta tags, titles, and descriptions would not need to be re-added. Site informational pages themselves (such as About Us, FAQ, etc) would need to be re-input but you just need to be sure to copy over any meta field info from the old site.
3) Ultimate has a built-in Google Sitemap generator and Google Product Feed generator. That can be very beneficial to SEO when utilized properly.
4) All that being said, any time you move from one cart platform to another, your URLs and URL structures do change. Google will eventually pick up on the new URLs once it re-crawls your website completely. It is a good idea to immediately generate a google sitemap and submit it to Google immediately after the move. This lets Google know that the URL structure of your website has changed site-wide and that will encourage them to re-crawl and drop old URLs and cache new ones.
However, there may be some leftover cached URLs in Google's search results from your old site. If an old URL is requested in a user's browser, Ultimate will take any non-existant URL and display a custom 404 page that contains a site map which will help your user find the page they were looking for easier. However, it is best for SEO to create a 301 redirect for any of your important or popular pages from the old URL to the new URL. This way, if a user visits the old URL or clicks on an old link in a search result, or pinterest pin for instance, it will automatically take them to the new URL of the same page. You can create 301 redirects by following this guide: http://www.shoppepro.com/support/knowledgebase/242/Creating-301-Redirects-in-Shoppe-Pro-Ultimate.html
5) As with any move from one platform to another, Google will inevitably encounter a 404 page or two while it drops the old URLs and crawls the new ones. This does have a slight possibility to negatively affect Page Ranking, however, if it does happen, it is only going to be temporary, and the move to the Ultimate platform will ultimately improve your SEO performance in the long run.
If you have any other concerns, please feel free to open a help desk ticket and we are more than happy to answer any questions you might have.
