You can set the timezones in Cloud Liunuz by editing the individual PHP versions conf file:

/opt/alt/php52/etc/php.ini
/opt/alt/php53/etc/php.ini
/opt/alt/php54/etc/php.ini
/opt/alt/php55/etc/php.ini

Then just specify the default timezone.

Example: date.timezone = "America/Toronto"

You can also give your customer the ability to modify it in the PHP selector option.

You would modify: /etc/cl.selector/php.conf

Directive = date.timezone
Default = America/Toronto
Type = Value
Comment = Change your server's timezone