OK, so I put some summary of what I read on SO about it :
URL rewriting for redirection :
Better to put that in the Apache configuration. using .htaccess is the most flexible way but your Apache conf must allow it, if not, set the rewriting in the Vhost file.
URL rewriting for ressource management :
When it's about managing not found contents, access right or getting clean URL for accessing dynamic contents, you need to set the rewriting in the script file of your app since it's where you have access to the API to handle this kind of things.
So both of the ways are complementary, and you will usually use both at the same time.