I have found (temporary) solution in this article or more precisely comments under.
Firstly installed sudo apt-get install imwheel
and then from
Olivier FEBWIN
It solved my problem with my Logitech M560 mouse!
imwheel -k -b "0 0 0 0 10 11" &
to make working side buttons
At least that works now 
But can someone tell me what should I write as command to create it as a start up program as I don't feel like it's the same as in the link above and I don't really want to mess something up...