Generally, you should use a package manager rather than install things from source. Also, copying files from one place to another is a good way to screw some things up.
What distro do you have? How does it suggest to install packages?
I'm running Linux Mint. The reason for installing from source was to have the latest version of AVR-GCC (4.5.1) as I also use this for other projects besides Arduino. It seems that the Arduino IDE expects the tools to be in a certain directory or path, but I don't know what that is. Linux Mint uses a similar package manager to Ubuntu to install packages.