3) The vhosts files should never be modified manually. Either you edit the master template that is used to create the files or you add your modifications to the apache directives field of the website.
1.- I need to fix a redirect problem, dunno why but one site add the rewrite directive to another file, :
If you add www redirect of a A domain
It changes the B.vhost file :S
Also I need to add "allowoveride all"
Where are the apaches directives to do this?