You really should stick to adding applications using Synaptic (or Aptitude or apt-get). If you can't find a program you need, try adding other repositories to your Synaptic. By default the Universe and Multiverse repositories are turned off because they're not officially supported by Canonical.
Turn them on and you'll find most software in Synaptic. That way you don't have to figure out paths and ini files, and removing is easy as well
k:
Read everything you need to know about Ubuntu:
in the (un)official Ubuntu guide!