Here's where I would start.
1 - Write down your objectives on paper (seriously the most important step) You need your building plan.
Once you know what you want to do and how you want it to function then this should tell you where to start next.
I think a site layout would be the first step. (SiteAssist)
Adjust the menu to suit (CCS Menu Builder)
Then add the database components (DataAssist)
Then add the e-cart (E-Cart)
then add security (Security Assist)
From what I can remember the e-cart PDF does a really good job of explaining how to setup the system, assuming you have some sort of site mapped out already. If not i'd suggest starting with Site Assist.
If you take the time to learn each component then building a e-commerce site is easy. Once you master this end you can then dive into customizing the site or adding the parts you need to your own web site.
Hope that helps!