In Linux, all applications are installed in the root file system where it is
protected. You determine where the root file system is at the time of
installation and cannot easily change it afterwards. You also determine the
size and file format. There are many variables when you install and if you
opt for a manual installation then you have complete control. It has its own
partition editor and everything. If you opt for automatic installation then
it will place your files in a logical pre-determined way.

The usual way is to place the root and home file systems on the same drive
or partition, but it is better to have separate root and home partitions. As
you learn more about Linux then you can work towards this goal.

The Linux root file system is akin to the \Windows folder plus \Program
Files and the Linux home folder is like \Documents and Settings. In Windows
when you try to access \Windows or \Program Files it will grey it out and
you won't have access until you tell it that it is okay to view it. Linux
takes this a step further. You can view the root structure, but can't change
it as a user. So you must first become root using su (Debian) or sudo
(Ubuntu), depending which distro you are using. Like in Windows you have
full access to home or Documents and Settings.

Unlike Windows, Linux has no registry so the root file system structure
takes care of that. Programmes and their dependencies are put into logical
folders that have become uniform over time. Their location is determined by
the scripts inside the installation file (deb or rpm). Unless you compile
your own source material then you have no control over the scripts. You
really have to know what you are doing to be working at this level. Just
rest assured that the developers do know what they are doing and place the
files where they can be found (because there is no central registry it has
to be this way).

Some applications can be installed to your home folder, but this usually
causes problems in th end. For example, you can install the Flock web
browser this way. It usually causes more problems for the user. There will
be no menu item unless you manually edit the menu and it will be unable to
find helper files, such as Flash unless you copy the flash libraries over or
in some cases create sym links. Generally speaking this is not the way to
go. If you can get the package from the repositories then it takes care of
all these details.

You can adjust the size of your partitions using a partition editor while
working from a Live CD (because you cannot work on a mounted file system),
if you run low on space. However, if your drive is small and there is no
extra space then you cannot take advantage of this. However, you can move
your entire installation to another drive and even set up separate root and
home partitions after installation once you know more. With Linux the sky is
the limit and knowledge is everything. Note: if you remove some of your
partitions then it may mess up the grub boot loader. The partitions in the
boot loader are relative. Removing one before will change its partition
number, but grub will be based on the original set up. You can re-write
grub, manually edit it or keep the relative boot order be only removing
partitions after the ones you are using or moving them with the partition
editor to keep the relative order.

You can also get extra space by cleaning out your caches and cleaning
installed packages (debs). You can do this with a utility like Computer
Janitor which comes with Ubuntu. You can also install Ubuntu Tweak from
Getdeb.net. It allows you to tweak Ubuntu to make life simpler.

I am glad that you are enjoying Ubuntu. The way to get the most out of it is
to learn how Linux works and think like a Linux user. What you know from
Windows becomes a liability because there are so many differences. It isn't
so much that one is better than the other and which one is, but the fact
that each is set up in a specific way based on the way it was developed,
each with a separate history. They only clash when we confuse them in our
own minds. One seems to be better because we are more comfortable with it
which really does not make it better at all, just more familiar. The
antidote for that is to immerse yourself in the unfamiliar and it becomes
familiar.