There are still a lot of options for what you could, might, and should do in your database. All are compatible with eCart, so that shouldn't be your focus.
Your focus should be how to best represent your data in your database. The best database design for your specific application is the best database design to use with eCart.
Are you doing inventory control? If you are they probably have to be listed as individual items in the database anyway so that you can track inventory on them individually. If not, you can probably organize them into a database structure that better suits your needs.
Additional price for larger items again is accomplished any number of ways. If you have individual items, then it is easy to see how you would accomodate individual prices.
If you are using a different database design with a single product and related options tables, then you can store an additional price with an option and integrate that into eCart as well. If the information can be retrieved from the database, then it can be used by eCart.