Multiple IDE instances
There is nothing special about it, it just works.

I strongly suggest to remove everything that is Arduino related from the repositories and have a minimal Java environment installed.

It is no problem to have a gcc build environment together with Arduino though. Even a gcc-avr build environment from the repositories is no problem. But don't install any Arduino or Java-rxtx from the repositories.

You can download the linux version and unpack it in a folder. 
Go to that folder where you unpacked the Arduino files and right-click on the 'arduino' file to create a shortcut. Move that shortcut to your Desktop.
Depending on the flavor of Ubuntu that you have, you can also create a starter and fill in the whole path of the 'arduino' file.  

Then you can start the Arduino IDE, and just click/activate that shortcut or starter again for another instance of the Arduino IDE. They will work independent of each other. You have to set the right board for each instance of course. A third one or more is also possible.

If you have trouble with shortcuts or starters, then you can even open a terminal and go to the unpacked files, type "./arduino" to start it. Open an other terminal (or new 'tab' in the terminal) and do the same.

You don't have to makes copies of the Arduino files, you don't have to make multiple shortcuts or starters. Just start a new instance by activating the shortcut or starter once more.

I recommend to use only the newest version (at the moment 1.8.3). But if you need to run an older version then you can download and unpack older versions in seperate folders. Be careful that you can not run different versions of the IDE at the same time. The Arduino IDE before 1.6.x differs too much from 1.8.x. All of them share the same ~/.arduino15 folder with settings and downloaded files, which can cause trouble when running a new version, then an older version and then a newer version again.