I managed to install MySQL 5.6 on obuntu 12.10 but now I need apache/php packages but when I try to install them thorough apt they try to install mysql-common (presumably 5.5) How to solve this?
The package mysql-common doesn't include any client nor server binaries. It is rather a module containing the libraries and modules for php5-mysql to work with. It shouldn't be a problem for you to install php5 or php5-mysql with that dependency as it won't interfere with your manual installed version of mysql-5.6 (if you did it as recommended in /opt or /usr/local/...). PHP5 will connect against the DB just OK. It is like using a mysql-client binary a bit older than the actual server.
If you run into problems with that setup, you would have to build a php-mysql module with 5.6 bindings yourself.