Hi Meirm
The bar you are reffering to is defined by your GTK theme, you can find a new theme and install it , your repo's should have some, also
Gnome-Look has plenty to choose from.
I'm guessing you see two different colours because one terminal is a root terminal using the default gtk theme for root user, the other is 'user' terminal which uses your chosen gtk theme.
The other option for changing colours is to edit the file in ~/.config/gtk*/gtk.css (if it exists) and change colour hex therein, good luck.