Noob question regarding software updates

I have been trying to understand if installing updates outside of the FreePBX Module Admin is recommended (or required even). I installed FreePBX 2.5 + Asterisk 1.4 via AsteriskNow, and have updated to 2.6.0.1.
I also installed Webmin to help with server admin, and I have several modules (both core CentOS modules and Asterisk 1.4) that WebMin says have pending updates, and my question is simple:
Is it OK to install all of the recomended package updates identified outside of the FrePBX admin interface?
Thanks to all for your support, I am new to Asterisk but lots of great info avaialble.
Chris
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Non Asterisk/FreePBX
Non Asterisk/FreePBX modules, I would update through Webmin, Asterisk/FreePBX udpate through the FreePBX setup/update module
Eugene Blanchard
Author of PBX in a Flash for Newbies and Introduction to Data Communications