Is it safe to update system packages using the operating system package manager ?

Yes, it is safe and moreover we recommend to use 'yum' (or 'apt-get' on Debian) to keep the system up-to-dated.

However some packages may conflict with Plesk or another software, they can be added into skip list. It is recommended to use the following settings:

• for up2date, add into /etc/sysconfig/rhn/up2date:
  
  pkgSkipList=kernel*;sendmail;bind-chroot;caching-nameserver;
• for yum, add into /etc/yum.conf:
  
  exclude kernel* sendmail bind-chroot caching-nameserver