With all respect sillyputty, I'm not sure whay they put a linux newb in charge of a Unix machine.
BE CAREFUL! What might look like junk (for example all that stuff in the /dev directory) is actually _very important_.
The whole point of a linux box is that you don't have to reboot for new configurations to take effect.
Linux is not like windows.
Consider the BSD boxes in Japan http://uptime.netcraft.net/up/today/top.avg.html
which have been running (without a reboot) for four years. Those systems are not simply rebooted. Use a gui tool like up2date to get all the RPMs for your system. It will install them while the system is up. You need to do this to take advantage of security patches because as UnSpawn (security mod here) might say, security is an ongoing task.
On the file structure, what are you not happy with? - there are standard directories for certain files but generally even a bad sysadmin won't change much there.
Go to your boss and ask to buy a good bok on Linux. If you don't feel that's a great idea now, look for stuff on google because most of the documentation is out there, not in books.
If you do decide to reboot, install Redhat 8.0, the blue curve theme is very pretty and redhat 7.2 was ... well, not so nice.