Prior to version 4.0 multiple instances of skype could be started just by clicking the same Skype icon again and again.
But in version 4.0 the steps are a bit different.
1. Install skype.
2. Skype stores its data in the directory $HOME/.Skype or ~/.Skype .
So create 2 copies of this directory and name them as ~/.Skype.first and ~/.Skype.second
3. Launch skype as :
$ skype --dbpath=~/.Skype.first $ skype --dbpath=~/.Skype.second
This will launch 2 instances of skype with the corresponding data directories. Use the same commands to create launchers on the desktop.