I have been an SEO expert for content based sites and have worked on many Optimizations for many websites. Now the present market demands for SEO for E-commerce based websites. Basically these websites are backed up by e-commerce software that allows them to create a shopping cart based on your category, descriptions etc. How do we generally go about performing SEO for e-commerce sites.
May be I misunderstood your question, but I treat the shop/cart as non existent and add, if necessary, product pages. All the rest should be "SEO as usual".
apply the same theories to content based sites as you do ecommerce sites, make good use of h1 and p tags and make sure each product page has unique meta content. Deep links work great with ecommerce store. the list goes on... If the ecommerce site is running oscommerce theres plenty on SEO mod's on the oscommerce contributions site.
Theres not any difference in the process although it is harder, dependant on the software the shopping carts built on.
Treat these sites as you treat your normal content sites. Keep your H1 tags, anchor tags and other tags which you consider will seo'ing your normal content sites intact. Then i guess you should go with deep linking as your linking building strategy.....
Let me which shopping cart software they have used.... You need to run the SEF URL module in the site server as well as need to add Meta Tag module in the site. Now write unique meta elements for every page. Create a sitemap and include all the URLs and submit them to various search engines. Now you can adopt general SEO strategies. I've been optimizing E-Commerce sites for quite a long time and I've got good results for my clients...