I need to update Apache and php (per WHM), but I am a bit paranoid that the automated process might blow away any of the changes I have made before.

So...

Is it safe to do it from inside the control panel, or should I use easyapache? Also, how long should the sites be down during the upgrade process?

Thanks!

it depends what changes you have made.. php.ini and httpd.conf should have any addons/settings you made you made still in them afterwards.. but you could login via ssh and make backup copies of those files before you start..

as for downtime if everything goes smoothly about ~1 minute when it restarts httpd a couple of times to reload and start using the new versions

Inside WHM and easyapache are the same thing. Personally I use easyapache via ssh. I have rarely have trouble and if I do running easyapache again fixes it.

Thanks for the help everyone - it went smoothly. I was just being paranoid.