The first thing you should do is visit the support page here on WebAssist.com (support/) and look through the resources there.
Personally the steps I follow when building a custom store would be as follows:
1.Map out the functionality and create a project scope - you really can't build something unless you know what it's suppose to look like and how it's suppose to function.
2. Build the database
3. Create the admin section so that I can manage the data that I'm going to be using on the front end and can get test data into the system.
4. Build the front end of the site
5. Once I'm happy with how it functions, wrap the security around the pages that need it.
I personally find it more difficult to take something like Blue Sky and retrofit what I need... most times it's easier to simply build it from scratch.