This is the stage where you code any special FCEs to handle situations unique to the site. It is also when you can install and configure any additional TYPO3 extensions.
Not much has been said on this site about creating templates and FCEs in TemplaVoila. It is not because that is no longer necessary. You will still need to understand and use the mapping interface of TemplaVoila if you really want to handle any design that that might come up. I recommend that you work through the tutorial Futuristic Template Building. It will walk you though how to produce templates and FCEs in TemplaVoila from scratch.