you need to be in the android group and have adb properly installed and preferrably the current version. I use a gentoo based linux system so this stuff isn't an issue for me.
Ubuntu and debian based systems are a little different. I really dislike the package management system and Ubuntu separates users from the actual "linux" part of linux. its like linux for n00bs. Not saying its a bad distro, its just not my distro of choice.
But, if you are booting up your device correctly, you should be able to do adb start-server and then do a adb remount (if rooted) then push the files to /system/app/
if you have just ran updates, reboot your computer. If you aren't picking up the device, try using other ports (usb ports can go into a suspend mode to save power and sometimes don't like to wake up, it also happens in windows)