Going in reverse order...

If you go with the default setting, it probably won't work. You've tied yourself i so many knots here you probably need a reinstall and a local LUG member to help you properly. At this stage, I don't know how many things have been altered or where.

Not everything needed by programs in windows goes in the one place. Just most of it.
Windows is monolithic and Linux is modular. This means that windows is smaller than linux for the same functionality, but that is crashes more and is easier to penetrate. Linux will run better, but some fiolk find the paradigm difficult to penetrate.

Linux install schemes usually put core binaries in /sbin, shared binaries in /usr/bin or /usr/share/bin (some distros have one, others have both) and other shared files go in /usr/share. Libraries go in their own set of directories also, depending on how they are to be shared. Block special devices go in /dev (for devfs). User specific details go in /home/username - often in a hidden file (so /home/yourname/rm * is a bad idea!) I wouldn't call this "thrown around" exactly. But it is more distributed than you are used to.

"I checked /usr/bin and didn't find anything there either" ... surely there was something there!

(Finding mozilla executables)
$ whereis mozilla
mozilla: /usr/bin/mozilla /usr/lib/mozilla /usr/share/man/man1/mozilla.1.gz

"whereis" looks for files in common binary locations.

I don't see why RHEL shouldn't do it the same way - but try whereis just in case.

"lrwxrwxrwx 1 root root 46 May 22 10:01 /usr/bin/system-control-network -> [etc]"
^^^^^^^^ this bit is the permissions. the l means it i a link. rwxrwxrwx means that anyone can use it without root access. ("rwx"=read-write-execute, the first set is for the owner=root, the second is for the group=root, and the last is for others=anybody.)

in terminal, as a user, just type "system-control-network" and press enter. The NDC thing should pop up. Activate your internet device and tell me when it prompts you for root password.

Hello,

Well I solved my shockwave problem. I just upgraded to a newer version of FireFox. I didn't read the directions of JAVA however so it's incorrectly configured. Is there a way to uninstall JAVA? It's from a .bin file. I made it into an executable and installed it.

Uninstall and reinstall firefox - I think that will be easiest.

Yeah - you could do it another way... like delete java from the plugins directory and such - but you'll just get confused again :)

Note: FFox has an extension which will allow only nominated sites to run java scripts on your machine. This is a must have. You'll also want adblock and a few other things.