You should find out how the system has been updated. If some update application like yum was used, then you can use that one to do the updates.
I once run into a RHEL server where yum was installed, but certain packages (MySQL for example) have been installed with a different procedure for some paranoid security reasons.
Run 'rpm -qi <packagename>' to see if the software that has to be updated is part of the RPM database at all.
Using yum for update will keep configuration files intact. In cases where new versions have a conflicting format for configuration files usually the older settings are saved in the same location with the .rpmsave extension appended.
Never be too proud to ask the IT senior manager for advice - it will be worse if you do it alone and you screw it all up.