Hi!
You are talking of two different things...
FreePBX modules add functionalities to FreePBX and are updated using "Module admin" from FreePBX itself.
On the other hand "yum update" update packages which are installed on the Linux distribution. Those can be updated using yum update or you can update them from System Admin (Pro?).
(Personally I prefer "yum update" since you see what gets updated.)
If you are using the distro then both should be safe to use and update...
Have a nice day!
Nick