You can use our automatic update system which is visible under the "Manage" tab, or you can do this manually.
To do this manually run
apt-get update && apt-get upgrade
Running this command is safe and cannot harm anything generally speaking. It is possible that Ploi is still telling you that there are still updates, in order to clear those you will need to run the command below here.
If you want to update all the kernel files as well:
apt-get update && apt-get dist-upgrade, if there are any packages eligible for upgrade then your server will display these.
apt-get dist-upgrade can be a dangerous command. There is a chance you will get asked questions about changed configuration files. If you want to stay in the safe zone select the option to keep the current installed one.