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, 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

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 Yup 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