I like to do these steps on each server listed once a month. You can do it as often or as little as you like.
These steps are specific to my servers, but only in terms of Debian and Ubuntu. Some things are specific for the setup here at Potlatch SD.
I have blanked out any passwords and usernames, those can be retrieved from documentation.
Web Server/Piler Server
Use Putty, it is the easiest SSH software out there.
At the initial prompt you need to su to do the update process.
$ apt-get update
$ apt-get upgrade
$ apt-get autoclean
$ apt-get autoremove
When that is complete then you can type exit twice to close out.
This is similar to above, but since it is Ubuntu you can use sudo instead of su at the beginning.
$ sudo apt-get update
$ sudo apt-get upgrade
If Koha was upgraded then you have to go and adjust the Circulation file to allow the scanners to work properly. instead of programming the scanners or changing the barcodes on every book now, I have modified the programming to adjust the barcode after scan at the elementary. The instructions are found on this blog under PSD Koha Circulation Barcode Modification.
$ sudo apt-get autoclean
$ sudo apt-get autoremove
When that is complete then you can type exit to close out.
PFSense Firwall/Gateway Server
This server checks for updates and will display if an update is needed on the dashboard. To upgrade you can click on the link and follow the instructions, the server will upgrade in place without much major interruption. I have done the update during the school day and only had the network disconnect for a few seconds while the service restarts. Some major updates require a restart so those should be done at the end of the day.
The Packages can be updated at anytime as well. These are add-ons that have been used to increase the effectiveness of the server. When you click on System -> Packages the next screen shows you what is installed. Anything that is highlighted in the version column has an update. To load that update click on the PKG button next to the row. That will install the update automatically.