You are learning which will be painful, no fear as a reinstall
is not hard to do. There will be many in your future

.
If you remember how you installed Flash? When new to Linux
you will notice it is easier to reinstall then to track down the
problem.
2) Do I need to be logged in as Root to install new packages?
The answer is yes. There is a mention that you can not cd into desktop, the reason
is that Linux is very verbose. Try cd Desktop.
As far as firefox login as root and then under tools check for update, update FF
that way. Then logout of root and the user FF will be updated.
HTH
Bigpaws