I would read this redbook. It has an example of how to code the JSPs - http://www.redbooks.ibm.com/redbooks/pdfs/sg247393.pdf.
Also if you're moving to FEP6, you'll also want to use the WebSphere Commerce tag libraries and some of the metatags so that the inline editing and some of the advanced store preview features work correctly.
Finally, I would engage your local IBM technical team since there are other customer who have done this before and you want to learn from their best practices.