I noticed the defrences now, installiing the sdk in windows automatically adds the needed libraries that includes flash player debugger and air to the sdk frameworks sub directory, I just tried it and it works fine in booth FDT and IntelliJ Idea Ultimate, but it has some issues in FDT, I will post a step by step guide later.
since it is working now, can anyone ask the site admin to declear sdk as supports linux, along with adding download link for the sdk "the arter install windows or mac" sdk. Regards, Saleh