Linux: Managing users, groups and applications

I am fairly new to linux admin so this may sound quite a noob question.

I have a VPS account with a root access.

I need to install Tomcat and Java on it and later other open source applications as well.
Installation for all of these is as simple as unzipping the .gz in a folder.

My questions are

A) Where should I keep all these programs?
In Windows, I typically have a folder called programs under c:\ where I unzip all applications.
I plan to have something similar here as well.
Currently, I have all these under apps folder under/root- which I am guessing is a bad idea. http://serverfault.com/questions/57962/whats-wrong-with-always-being-root
Right now I am planning to put them under /opt

B) To what group should Tom belong to ?
I would need a user - say Tom who can simply execute these programs.
Do I need to create a new group? or just add Tom to some existing group ?

C) Finally- Am I doing something really stupid by installing all these application by simply unzipping them?
I mean an alternate way would be to use Yum or RPM or something like that to install these applications.
Given my familiarity and (tight budget) that seems too much to me.
I feel uncomfortable running commands which i don't understand too well

From serverfault RN

• A) Read the Filesystem Hierarchy Standard.

  B) Tom should not be running these programs. They should be run by root, in the background.

  C) Yes. Packages for a distro are tuned to work efficiently within the distro and with other packages in the distro.

  RUTE

  RHEL documentation

  Money? CentOS.

  RN : I thought it was a bad idea to start programs like Tomcat as a root http://serverfault.com/questions/57962/whats-wrong-with-always-being-root

  Ignacio Vazquez-Abrams : Most programs either drop privileges after starting, or are actually run via wrappers that force it to be run as another user. But in either case they are started *by* root, even though they don't run *as* root.
  From Ignacio Vazquez-Abrams

• Learn to use your package manager. They are good, they will do things right more often than not. Windows Doesn't have a sane package manager. By using your package manager it can tell you when security updates become available. It allows for easy removal. Other people who are familiar with this distribution will be familiar with the locations things have been installed to. You will be more able to use your distro's online documentation and community. These will be less available if you do everything yourself. Only do it the manual way if your distro doesn't provide what you need (and even then I'd recommend learning to package it yourself and still using the package manager).

  From xenoterracide