Hi Laura.
For the structure take a look on this guide. http://searchengineland.com/best-practices-in-e-commerce-seo-176921 At Question 8 you have good recomendatios for categories estructure.
About using subdomains - domains - folders, I prefer using folders, so you will have the same domain authority in all folders. Anyway you can read this excellent article about it: http://moz.com/blog/understanding-root-domains-subdomains-vs-subfolders-microsites
Good Luck!