I use Lubuntu 12.04 and a gtk2 theme, Elegant Arch.
With such a theme, gtk2 applications like Thunar will be themed, while others like Nautilus, would be not (see this question ant the images there).
Because I wanted to theme gtk3 applications like Nautilus, Audacious etc., I have copied the "gtk-3" folder from the main folder of a gtk3 theme into the main folder of my Elegant arch theme, which is in home/username/themes. Using the gtk3 folder from this full flat theme I got a pretty similar look in gtk2 and gtk 3 apps.
Lubuntu Desktop Center, Ubuntu Desktop Center, Network Options and other such apps are now themed (before they were not). Even Update Manager is.
But why is Synaptic Manager not themed?
Best Answer
The application you are opening is one that needs root privileges. You could also link the files to use them: