In answer to your points:

To find all the files associated with a package, type dpkg -L <name of
package> For instance, on my system, here is what I see for google chrome:

jjs@einstein:~$ dpkg -L google-chrome-stable
/.
/etc
/etc/cron.daily
/etc/cron.daily/google-chrome
/opt
/opt/google
/opt/google/chrome
/opt/google/chrome/xdg-settings
/opt/google/chrome/chrome.pak
/opt/google/chrome/libgcflashplayer.so
<...several hundred lines trimmed for sake of space...>
/usr/share/gnome-control-center/default-apps/google-chrome.xml
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/google-chrome.1
/usr/bin/google-chrome
jjs@einstein:~$


As to installing software where you want, you can always do that as long
as you know how. But it's not a good idea generally. The existing file
locations have been carefully thought out and conform to LFS and ubuntu
standards. Can you give an example of a piece of software that you'd
like to install in a non-standard location?

When you uninstall a package it removes all original components, but
does not remove files which you have modified. Which is a very good
thing, as I might need my specially tweaked config file for future
reference. If you want to remove all traces, you'll have to do it on
purpose, and one way to accomplish this is with the command "dpkg
--purge <package name>"

I ran dpkg command and it worked like a charm.
Until now, I have not found it necessary to install software according to my
wishes. But, I thought that it would be good to have control on software
installation rather than ubuntu doing it for me. Once I get more familiar with
linux aura, I might play with the settings, just for the sake of fun...lol
I was thinking of installing a simulation software and therefore, I might need
to install the software in a specifc directory. So, if I would need that, then I
will start searching on the internet for more understanding and post questions
again.

Ubuntu, and Linux generally, prefers standard, predictable order to
unorganized freedom (which is another word for chaos). Things just go
better that way.

Why would you need to "find all files associated with any software"?
If there is a problem far better to completely uninstall (an option
with Synaptic) and reinstall. If you have an insatiable curiousity
about all things tech then do your homework with Google searches and
you will find enough information to keep you busy for a long, long
time. Digest that and become an expert!

If you were able to install software where ever you want to it would
produce a file structure unique to your own machine. After a few
months you wouldn't know where to find anything - unless you are a
meticulous documenter, but what's the point? Don't re-invent the
wheel! My advice is to do it the safe, easy way by letting the system
make these decisions for you.

Am I right in my understanding, that you can decide to put software
you've created yourself (Including scripts. Especially scripts.)
wherever you want to? It's not the operating system that dictates where
the software must go but the package itself?

Having said that, most if not all linux software seems to be extremely
consistent - are developers that well behaved or is there something more
than standards to enforce it?

Each distribution has its own package management and organisation. Where the
package manager puts things varies by distribution and not by developer.
Each distribution has its own repositories and maintainer who enforce the
standards. It is all in the family so to speak.

one point to mention is that linux security is based on
permissions and therefore the best place to install stuff is in the
dictated folders. If you install from source you can install into the
/usr/local/bin folder.

Thank you all for your replies and contributing to the discussion.
So, I guess the conclusion is that let linux install according to its own wishes
and do not interrupt it.

As you said that package manager puts things by distros and not by developer.
Does that mean that if I make a software application I would need to abide by
the rules of that distros?

No. Software developers make software and package maintainers decide to
include it or not. There is much Linux software on Sourceforge and other
places that is not in the Ubuntu repositories. Obviously it is in the best
interests of promoting your software to have it in the repos.

Not having it in the repos need not stop developers, however. They can
package it to meet the specifications of various distributions and then have
debs or rpms on their site. In Ubuntu's case they could make a PPA or for
all distributions they could add a source to your sources file.

The problem is in the number of distributions and package managers. Another
problem is the way that Linux handles dependencies. Generally you can't have
multiple instances of a dependency since their is no registry file to track
them as in Windows. Shared dependencies reduce space, but often lead to
dependency conflicts that are difficult or impossible to resolve, forcing
the user to choose between two applications. The repositories mitigate this
by ensuring the dependencies are of the same version. If you stick with the
sources maintained by the developer you seldom run into dependency problems,
but if you add to the sources and install outside packages then you increase
the risk of dependency problems.

I do not understand all things here, either, but surely by uninstalling a
program with sudo aptitude remove you do not uninstall it completely. All the
settings are saved and when you reinstall the program with sudo aptitude install
all the previous settings work again. You can completely remove the program
with sudo aptitude purge.

I only install trusted and tested software from
Applications / Ubuntu Software Center,
(and thats where to uninstall from too)

one trouble with windows is all those buggy virusey *.exe files
hanging around the internet.